Index

_

__call__() (toil.batchSystems.abstractBatchSystem.OptionSetter method) (toil.batchSystems.awsBatch.OptionSetter method) (toil.batchSystems.kubernetes.OptionSetter method) (toil.batchSystems.mesos.batchSystem.OptionSetter method) (toil.batchSystems.options.OptionSetter method) (toil.batchSystems.singleMachine.OptionSetter method) (toil.batchSystems.slurm.OptionSetter method) (toil.jobStores.aws.jobStore.InnerClass method) (toil.leader.LocalThrottle method) (toil.lib.objects.InnerClass method) (toil.lib.throttle.LocalThrottle method) (toil.lib.throttle.throttle method) (toil.provisioners.clusterScaler.throttle method) (toil.serviceManager.LocalThrottle method) (toil.serviceManager.throttle method) (toil.test.batchSystems.batch_system_plugin_test.OptionSetter method) __copy__() (toil.batchSystems.abstractBatchSystem.Requirer method) (toil.batchSystems.awsBatch.Requirer method) (toil.batchSystems.kubernetes.Requirer method) (toil.batchSystems.singleMachine.Requirer method) (toil.batchSystems.slurm.Requirer method) (toil.job.Requirer method) (toil.test.batchSystems.batchSystemTest.Requirer method) __deepcopy__() (toil.batchSystems.abstractBatchSystem.Requirer method) (toil.batchSystems.awsBatch.Requirer method) (toil.batchSystems.kubernetes.Requirer method) (toil.batchSystems.singleMachine.Requirer method) (toil.batchSystems.slurm.Requirer method) (toil.job.Requirer method) (toil.test.batchSystems.batchSystemTest.Requirer method) __del__() (toil.batchSystems.abstractBatchSystem.DeferredFunctionManager method) (toil.deferred.DeferredFunctionManager method) (toil.fileStores.cachingFileStore.CachingFileStore method) (toil.fileStores.nonCachingFileStore.NonCachingFileStore method) (toil.worker.DeferredFunctionManager method) __enter__() (toil.batchSystems.abstractBatchSystem.Toil method) (toil.batchSystems.awsBatch.Toil method) (toil.batchSystems.cleanup_support.Toil method) (toil.batchSystems.cleanup_support.WorkerCleanupContext method) (toil.batchSystems.kubernetes.Toil method) (toil.batchSystems.singleMachine.Toil method) (toil.common.RealtimeLogger method) (toil.common.Toil method) (toil.cwl.cwltoil.Toil method) (toil.deferred.RealtimeLogger method) (toil.fileStores.abstractFileStore.Toil method) (toil.job.Toil method) (toil.jobStores.aws.jobStore.panic method) (toil.jobStores.aws.jobStore.ReadablePipe method) (toil.jobStores.aws.jobStore.WritablePipe method) (toil.jobStores.googleJobStore.ReadablePipe method) (toil.jobStores.googleJobStore.WritablePipe method) (toil.jobStores.utils.ReadablePipe method) (toil.jobStores.utils.WritablePipe method) (toil.lib.ec2.panic method) (toil.lib.exceptions.panic method) (toil.lib.throttle.throttle method) (toil.provisioners.clusterScaler.throttle method) (toil.realtimeLogger.RealtimeLogger method) (toil.server.wes.tasks.Toil method) (toil.serviceManager.throttle method) (toil.test.ApplianceTestSupport.Appliance method) (toil.test.batchSystems.batch_system_plugin_test.Toil method) (toil.test.batchSystems.batchSystemTest.Toil method) (toil.test.jobStores.jobStoreTest.Toil method) (toil.test.lib.dockerTest.Toil method) (toil.test.mesos.helloWorld.Toil method) (toil.test.options.options.Toil method) (toil.test.sort.restart_sort.RealtimeLogger method) (toil.test.sort.restart_sort.Toil method) (toil.test.sort.sort.RealtimeLogger method) (toil.test.sort.sort.Toil method) (toil.test.sort.sortTest.Toil method) (toil.test.src.autoDeploymentTest.ApplianceTestSupport.Appliance method) (toil.test.src.busTest.Toil method) (toil.test.src.environmentTest.Toil method) (toil.test.src.fileStoreTest.RealtimeLogger method) (toil.test.src.fileStoreTest.Toil method) (toil.test.src.importExportFileTest.Toil method) (toil.test.src.jobDescriptionTest.Toil method) (toil.test.src.jobFileStoreTest.Toil method) (toil.test.src.jobTest.Toil method) (toil.test.src.miscTests.panic method) (toil.test.src.realtimeLoggerTest.RealtimeLogger method) (toil.test.src.restartDAGTest.Toil method) (toil.test.src.toilContextManagerTest.Toil method) (toil.test.utils.toilKillTest.Toil method) (toil.test.utils.utilsTest.Toil method) (toil.utils.toilClean.Toil method) (toil.utils.toilDebugFile.Toil method) (toil.utils.toilDebugJob.Toil method) (toil.utils.toilKill.Toil method) (toil.utils.toilStats.Toil method) (toil.utils.toilStatus.Toil method) (toil.wdl.wdltoil.Toil method) (toil.worker.Toil method) __eq__() (toil.batchSystems.abstractBatchSystem.Config method) (toil.batchSystems.awsBatch.Config method) (toil.batchSystems.cleanup_support.Config method) (toil.batchSystems.kubernetes.Config method) (toil.batchSystems.local_support.Config method) (toil.batchSystems.mesos.Shape method) (toil.batchSystems.singleMachine.Config method) (toil.common.Config method) (toil.job.Config method) (toil.job.TemporaryID method) (toil.jobStores.abstractJobStore.Config method) (toil.jobStores.fileJobStore.TemporaryID method) (toil.leader.Config method) (toil.leader.TemporaryID method) (toil.lib.ec2nodes.InstanceType method) (toil.lib.generatedEC2Lists.InstanceType method) (toil.provisioners.abstractProvisioner.Shape method) (toil.provisioners.aws.awsProvisioner.InstanceType method) (toil.provisioners.aws.awsProvisioner.Shape method) (toil.provisioners.clusterScaler.Config method) (toil.provisioners.clusterScaler.Shape method) (toil.provisioners.gceProvisioner.Shape method) (toil.test.batchSystems.batchSystemTest.Config method) (toil.test.batchSystems.test_slurm.Config method) (toil.test.jobStores.jobStoreTest.Config method) (toil.test.jobStores.jobStoreTest.TemporaryID method) (toil.test.provisioners.clusterScalerTest.Config method) (toil.test.provisioners.clusterScalerTest.Shape method) (toil.test.src.jobDescriptionTest.TemporaryID method) (toil.test.src.workerTest.Config method) (toil.test.utils.utilsTest.Config method) (toil.utils.toilDebugFile.Config method) (toil.utils.toilDebugJob.Config method) (toil.utils.toilKill.Config method) (toil.utils.toilStats.Config method) (toil.utils.toilStatus.Config method) (toil.wdl.wdltoil.TemporaryID method) (toil.worker.Config method) __exit__() (toil.batchSystems.abstractBatchSystem.Toil method) (toil.batchSystems.awsBatch.Toil method) (toil.batchSystems.cleanup_support.Toil method) (toil.batchSystems.cleanup_support.WorkerCleanupContext method) (toil.batchSystems.kubernetes.Toil method) (toil.batchSystems.singleMachine.Toil method) (toil.common.RealtimeLogger method) (toil.common.Toil method) (toil.cwl.cwltoil.Toil method) (toil.deferred.RealtimeLogger method) (toil.fileStores.abstractFileStore.Toil method) (toil.job.Toil method) (toil.jobStores.aws.jobStore.panic method) (toil.jobStores.aws.jobStore.ReadablePipe method) (toil.jobStores.aws.jobStore.WritablePipe method) (toil.jobStores.googleJobStore.ReadablePipe method) (toil.jobStores.googleJobStore.WritablePipe method) (toil.jobStores.utils.ReadablePipe method) (toil.jobStores.utils.WritablePipe method) (toil.lib.ec2.panic method) (toil.lib.exceptions.panic method) (toil.lib.throttle.throttle method) (toil.provisioners.clusterScaler.throttle method) (toil.realtimeLogger.RealtimeLogger method) (toil.server.wes.tasks.Toil method) (toil.serviceManager.throttle method) (toil.test.ApplianceTestSupport.Appliance method) (toil.test.batchSystems.batch_system_plugin_test.Toil method) (toil.test.batchSystems.batchSystemTest.Toil method) (toil.test.jobStores.jobStoreTest.Toil method) (toil.test.lib.dockerTest.Toil method) (toil.test.mesos.helloWorld.Toil method) (toil.test.options.options.Toil method) (toil.test.sort.restart_sort.RealtimeLogger method) (toil.test.sort.restart_sort.Toil method) (toil.test.sort.sort.RealtimeLogger method) (toil.test.sort.sort.Toil method) (toil.test.sort.sortTest.Toil method) (toil.test.src.autoDeploymentTest.ApplianceTestSupport.Appliance method) (toil.test.src.busTest.Toil method) (toil.test.src.environmentTest.Toil method) (toil.test.src.fileStoreTest.RealtimeLogger method) (toil.test.src.fileStoreTest.Toil method) (toil.test.src.importExportFileTest.Toil method) (toil.test.src.jobDescriptionTest.Toil method) (toil.test.src.jobFileStoreTest.Toil method) (toil.test.src.jobTest.Toil method) (toil.test.src.miscTests.panic method) (toil.test.src.realtimeLoggerTest.RealtimeLogger method) (toil.test.src.restartDAGTest.Toil method) (toil.test.src.toilContextManagerTest.Toil method) (toil.test.utils.toilKillTest.Toil method) (toil.test.utils.utilsTest.Toil method) (toil.utils.toilClean.Toil method) (toil.utils.toilDebugFile.Toil method) (toil.utils.toilDebugJob.Toil method) (toil.utils.toilKill.Toil method) (toil.utils.toilStats.Toil method) (toil.utils.toilStatus.Toil method) (toil.wdl.wdltoil.Toil method) (toil.worker.Toil method) __get__() (toil.jobStores.aws.jobStore.InnerClass method) (toil.lib.objects.InnerClass method) __getattr__() (in module toil.batchSystems.registry) (toil.batchSystems.kubernetes.KubernetesBatchSystem.DecoratorWrapper method) (toil.realtimeLogger.RealtimeLoggerMetaclass method) __getattribute__() (toil.lib.expando.MagicExpando method) (toil.worker.MagicExpando method) __getstate__() (toil.batchSystems.abstractBatchSystem.Requirer method) (toil.batchSystems.awsBatch.Requirer method) (toil.batchSystems.kubernetes.Requirer method) (toil.batchSystems.singleMachine.Requirer method) (toil.batchSystems.slurm.Requirer method) (toil.job.Requirer method) (toil.test.batchSystems.batchSystemTest.Requirer method) __gt__() (toil.batchSystems.mesos.batchSystem.MesosShape method) (toil.batchSystems.mesos.MesosShape method) (toil.batchSystems.mesos.Shape method) (toil.provisioners.abstractProvisioner.Shape method) (toil.provisioners.aws.awsProvisioner.Shape method) (toil.provisioners.clusterScaler.Shape method) (toil.provisioners.gceProvisioner.Shape method) (toil.test.provisioners.clusterScalerTest.Shape method) __hash__() (toil.batchSystems.abstractBatchSystem.Config method) (toil.batchSystems.awsBatch.Config method) (toil.batchSystems.cleanup_support.Config method) (toil.batchSystems.kubernetes.Config method) (toil.batchSystems.local_support.Config method) (toil.batchSystems.mesos.Shape method) (toil.batchSystems.singleMachine.Config method) (toil.common.Config method) (toil.job.Config method) (toil.job.TemporaryID method) (toil.jobStores.abstractJobStore.Config method) (toil.jobStores.fileJobStore.TemporaryID method) (toil.leader.Config method) (toil.leader.TemporaryID method) (toil.provisioners.abstractProvisioner.Node method) (toil.provisioners.abstractProvisioner.Shape method) (toil.provisioners.aws.awsProvisioner.Node method) (toil.provisioners.aws.awsProvisioner.Shape method) (toil.provisioners.clusterScaler.Config method) (toil.provisioners.clusterScaler.Shape method) (toil.provisioners.gceProvisioner.Node method) (toil.provisioners.gceProvisioner.Shape method) (toil.provisioners.node.Node method) (toil.test.batchSystems.batchSystemTest.Config method) (toil.test.batchSystems.test_slurm.Config method) (toil.test.jobStores.jobStoreTest.Config method) (toil.test.jobStores.jobStoreTest.TemporaryID method) (toil.test.provisioners.clusterScalerTest.Config method) (toil.test.provisioners.clusterScalerTest.Node method) (toil.test.provisioners.clusterScalerTest.Shape method) (toil.test.src.jobDescriptionTest.TemporaryID method) (toil.test.src.workerTest.Config method) (toil.test.utils.utilsTest.Config method) (toil.utils.toilDebugFile.Config method) (toil.utils.toilDebugJob.Config method) (toil.utils.toilKill.Config method) (toil.utils.toilStats.Config method) (toil.utils.toilStatus.Config method) (toil.wdl.wdltoil.TemporaryID method) (toil.worker.Config method)

__iter__() (toil.lib.iterables.concat method) (toil.resource.concat method) (toil.test.concat method) (toil.test.src.autoDeploymentTest.concat method) __ne__() (toil.job.TemporaryID method) (toil.jobStores.fileJobStore.TemporaryID method) (toil.leader.TemporaryID method) (toil.test.jobStores.jobStoreTest.TemporaryID method) (toil.test.src.jobDescriptionTest.TemporaryID method) (toil.wdl.wdltoil.TemporaryID method) __reduce__() (toil.cwl.cwltoil.Promise method) (toil.job.EncapsulatedJob method) (toil.job.Promise method) (toil.wdl.wdltoil.Promise method) __repr__ (toil.deferred.DeferredFunction attribute) (toil.job.DeferredFunction attribute) __repr__() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.abstractBatchSystem.ResourcePool method) (toil.batchSystems.abstractBatchSystem.ResourceSet method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.kubernetes.ResourcePool method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.mesos.Shape method) (toil.batchSystems.singleMachine.JobDescription method) (toil.batchSystems.singleMachine.ResourcePool method) (toil.batchSystems.singleMachine.ResourceSet method) (toil.bus.JobStatus method) (toil.cwl.cwltoil.DefaultWithSource method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.cwltoil.JustAValue method) (toil.cwl.cwltoil.ResolveSource method) (toil.cwl.cwltoil.StepValueFrom method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.job.TemporaryID method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.fileJobStore.TemporaryID method) (toil.leader.JobDescription method) (toil.leader.TemporaryID method) (toil.provisioners.abstractProvisioner.Node method) (toil.provisioners.abstractProvisioner.Shape method) (toil.provisioners.aws.awsProvisioner.Node method) (toil.provisioners.aws.awsProvisioner.Shape method) (toil.provisioners.clusterScaler.JobDescription method) (toil.provisioners.clusterScaler.Shape method) (toil.provisioners.gceProvisioner.Node method) (toil.provisioners.gceProvisioner.Shape method) (toil.provisioners.node.Node method) (toil.server.wes.amazon_wes_utils.JobStatus method) (toil.server.wes.toil_backend.JobStatus method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.jobStores.jobStoreTest.TemporaryID method) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.Node method) (toil.test.provisioners.clusterScalerTest.Shape method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.jobDescriptionTest.TemporaryID method) (toil.test.src.workerTest.FileJobStore method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStatus.JobDescription method) (toil.wdl.wdltoil.TemporaryID method) (toil.worker.JobDescription method) __setstate__() (toil.job.UnfulfilledPromiseSentinel static method) __slots__ (toil.lib.ec2nodes.InstanceType attribute) (toil.lib.generatedEC2Lists.InstanceType attribute) (toil.provisioners.aws.awsProvisioner.InstanceType attribute) __str__() (toil.batchSystems.abstractBatchSystem.InsufficientSystemResources method) (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.abstractBatchSystem.ResourcePool method) (toil.batchSystems.abstractBatchSystem.ResourceSet method) (toil.batchSystems.abstractGridEngineBatchSystem.CalledProcessErrorStderr method) (toil.batchSystems.awsBatch.InsufficientSystemResources method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.DeadlockException method) (toil.batchSystems.gridengine.CalledProcessErrorStderr method) (toil.batchSystems.kubernetes.InsufficientSystemResources method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.kubernetes.ResourcePool method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.mesos.Shape method) (toil.batchSystems.singleMachine.InsufficientSystemResources method) (toil.batchSystems.singleMachine.JobDescription method) (toil.batchSystems.singleMachine.ResourcePool method) (toil.batchSystems.singleMachine.ResourceSet method) (toil.batchSystems.slurm.CalledProcessErrorStderr method) (toil.batchSystems.slurm.InsufficientSystemResources method) (toil.batchSystems.torque.CalledProcessErrorStderr method) (toil.cwl.cwltoil.FailedJobsException method) (toil.cwl.cwltoil.InsufficientSystemResources method) (toil.cwl.cwltoil.Job method) (toil.cwl.cwltoil.JobTooBigError method) (toil.cwl.cwltoil.ToilTool method) (toil.deferred.DeferredFunction method) (toil.exceptions.FailedJobsException method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.DeferredFunction method) (toil.job.Job method) (toil.job.JobDescription method) (toil.job.TemporaryID method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.Job method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.jobStores.fileJobStore.TemporaryID method) (toil.leader.DeadlockException method) (toil.leader.FailedJobsException method) (toil.leader.JobDescription method) (toil.leader.TemporaryID method) (toil.lib.ec2nodes.InstanceType method) (toil.lib.generatedEC2Lists.InstanceType method) (toil.lib.misc.CalledProcessErrorStderr method) (toil.provisioners.abstractProvisioner.Node method) (toil.provisioners.abstractProvisioner.Shape method) (toil.provisioners.aws.awsProvisioner.InstanceType method) (toil.provisioners.aws.awsProvisioner.Node method) (toil.provisioners.aws.awsProvisioner.Shape method) (toil.provisioners.clusterScaler.JobDescription method) (toil.provisioners.clusterScaler.JobTooBigError method) (toil.provisioners.clusterScaler.NodeReservation method) (toil.provisioners.clusterScaler.Shape method) (toil.provisioners.gceProvisioner.Node method) (toil.provisioners.gceProvisioner.Shape method) (toil.provisioners.node.Node method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.InsufficientSystemResources method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.batchSystems.test_slurm.CalledProcessErrorStderr method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.jobStores.jobStoreTest.TemporaryID method) (toil.test.lib.dockerTest.FailedJobsException method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.Node method) (toil.test.provisioners.clusterScalerTest.NodeReservation method) (toil.test.provisioners.clusterScalerTest.Shape method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.FailedJobsException method) (toil.test.sort.sortTest.Job method) (toil.test.src.autoDeploymentTest.FailedJobsException method) (toil.test.src.busTest.FailedJobsException method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.FailedJobsException method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.FailedJobsException method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.FailedJobsException method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.FailedJobsException method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.jobDescriptionTest.TemporaryID method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.DeadlockException method) (toil.test.src.jobServiceTest.FailedJobsException method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.FailedJobsException method) (toil.test.src.jobTest.Job method) (toil.test.src.miscTests.CalledProcessErrorStderr method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.FailedJobsException method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.FailedJobsException method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.FailedJobsException method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.src.workerTest.JobDescription method) (toil.test.utils.utilsTest.Job method) (toil.toilState.JobDescription method) (toil.utils.toilStats.Job method) (toil.utils.toilStatus.JobDescription method) (toil.wdl.wdltoil.InsufficientSystemResources method) (toil.wdl.wdltoil.Job method) (toil.wdl.wdltoil.JobTooBigError method) (toil.wdl.wdltoil.TemporaryID method) (toil.worker.Job method) (toil.worker.JobDescription method)

A

a() (in module toil.test.src.promisesTest) a_long_time (in module toil.lib.ec2) a_short_time (in module toil.lib.ec2) (in module toil.provisioners.abstractProvisioner) (in module toil.provisioners.aws.awsProvisioner) (in module toil.provisioners.node) AbstractAWSAutoscaleTest (class in toil.test.provisioners.aws.awsProvisionerTest) AbstractBatchSystem (class in toil.batchSystems.abstractBatchSystem) (class in toil.leader) (class in toil.provisioners.clusterScaler) (class in toil.test.batchSystems.batch_system_plugin_test) (class in toil.test.batchSystems.batchSystemTest) (class in toil.test.provisioners.clusterScalerTest) AbstractClusterTest (class in toil.test.cactus.test_cactus_integration) (class in toil.test.provisioners.aws.awsProvisionerTest) (class in toil.test.provisioners.clusterTest) (class in toil.test.wdl.wdltoil_test_kubernetes) AbstractEncryptedJobStoreTest (class in toil.test.jobStores.jobStoreTest) AbstractEncryptedJobStoreTest.Test (class in toil.test.jobStores.jobStoreTest) AbstractFileStore (class in toil.batchSystems.abstractBatchSystem) (class in toil.cwl.cwltoil) (class in toil.cwl.utils) (class in toil.fileStores.abstractFileStore) (class in toil.fileStores.cachingFileStore) (class in toil.fileStores.nonCachingFileStore) (class in toil.test.cwl.cwlTest) (class in toil.wdl.wdltoil) (class in toil.worker) AbstractGCEAutoscaleTest (class in toil.test.provisioners.gceProvisionerTest) AbstractGridEngineBatchSystem (class in toil.batchSystems.abstractGridEngineBatchSystem) (class in toil.batchSystems.gridengine) (class in toil.batchSystems.htcondor) (class in toil.batchSystems.lsf) (class in toil.batchSystems.slurm) (class in toil.batchSystems.torque) AbstractGridEngineBatchSystem.GridEngineThread (class in toil.batchSystems.abstractGridEngineBatchSystem) (class in toil.batchSystems.gridengine) (class in toil.batchSystems.htcondor) (class in toil.batchSystems.lsf) (class in toil.batchSystems.slurm) (class in toil.batchSystems.torque) AbstractGridEngineBatchSystem.GridEngineThreadException, [1], [2], [3], [4], [5] AbstractJobStore (class in toil.cwl.cwltoil) (class in toil.cwl.utils) (class in toil.fileStores.abstractFileStore) (class in toil.fileStores.cachingFileStore) (class in toil.fileStores.nonCachingFileStore) (class in toil.jobStores.abstractJobStore) (class in toil.jobStores.aws.jobStore) (class in toil.jobStores.fileJobStore) (class in toil.jobStores.googleJobStore) (class in toil.leader) (class in toil.serviceManager) (class in toil.toilState) (class in toil.utils.toilStats) (class in toil.wdl.wdltoil) (class in toil.worker) AbstractJobStoreTest (class in toil.test.jobStores.jobStoreTest) AbstractJobStoreTest.Test (class in toil.test.jobStores.jobStoreTest) AbstractProvisioner (class in toil.leader) (class in toil.provisioners.abstractProvisioner) (class in toil.provisioners.aws.awsProvisioner) (class in toil.provisioners.clusterScaler) (class in toil.provisioners.gceProvisioner) (class in toil.test.provisioners.clusterScalerTest) AbstractProvisioner.InstanceConfiguration (class in toil.leader) (class in toil.provisioners.abstractProvisioner) (class in toil.provisioners.aws.awsProvisioner) (class in toil.provisioners.clusterScaler) (class in toil.provisioners.gceProvisioner) (class in toil.test.provisioners.clusterScalerTest) AbstractScalableBatchSystem (class in toil.batchSystems.abstractBatchSystem) (class in toil.batchSystems.mesos.batchSystem) (class in toil.provisioners.clusterScaler) (class in toil.test.provisioners.clusterScalerTest) AbstractStateStore (class in toil.server.utils) AbstractToilWESServerTest (class in toil.test.server.serverTest) accelerator_satisfies() (in module toil.batchSystems.singleMachine) (in module toil.job) AcceleratorRequirement (class in toil.batchSystems.abstractGridEngineBatchSystem) (class in toil.batchSystems.htcondor) (class in toil.batchSystems.singleMachine) (class in toil.cwl.cwltoil) (class in toil.job) (class in toil.lib.accelerators) (class in toil.wdl.wdltoil) accelerators (toil.batchSystems.abstractBatchSystem.Requirer property) (toil.batchSystems.awsBatch.Requirer property) (toil.batchSystems.kubernetes.Requirer property) (toil.batchSystems.singleMachine.Requirer property) (toil.batchSystems.slurm.Requirer property) (toil.cwl.cwltoil.Job property) (toil.fileStores.abstractFileStore.Job property) (toil.fileStores.cachingFileStore.Job property) (toil.fileStores.nonCachingFileStore.Job property) (toil.job.Job property) (toil.job.RequirementsDict attribute) (toil.job.Requirer property) (toil.jobStores.aws.jobStore.Job property) (toil.test.batchSystems.batchSystemTest.Job property) (toil.test.batchSystems.batchSystemTest.Requirer property) (toil.test.jobStores.jobStoreTest.Job property) (toil.test.lib.dockerTest.Job property) (toil.test.mesos.helloWorld.Job property) (toil.test.mesos.stress.Job property) (toil.test.provisioners.restartScript.Job property) (toil.test.sort.restart_sort.Job property) (toil.test.sort.sort.Job property) (toil.test.sort.sortTest.Job property) (toil.test.src.busTest.Job property) (toil.test.src.checkpointTest.Job property) (toil.test.src.deferredFunctionTest.Job property) (toil.test.src.environmentTest.Job property) (toil.test.src.fileStoreTest.Job property) (toil.test.src.helloWorldTest.Job property) (toil.test.src.importExportFileTest.Job property) (toil.test.src.jobDescriptionTest.Job property) (toil.test.src.jobEncapsulationTest.Job property) (toil.test.src.jobFileStoreTest.Job property) (toil.test.src.jobServiceTest.Job property) (toil.test.src.jobTest.Job property) (toil.test.src.promisedRequirementTest.Job property) (toil.test.src.promisesTest.Job property) (toil.test.src.realtimeLoggerTest.Job property) (toil.test.src.restartDAGTest.Job property) (toil.test.src.resumabilityTest.Job property) (toil.test.src.retainTempDirTest.Job property) (toil.test.src.toilContextManagerTest.Job property) (toil.test.src.userDefinedJobArgTypeTest.Job property) (toil.test.utils.utilsTest.Job property) (toil.utils.toilStats.Job property) (toil.wdl.wdltoil.Job property) (toil.worker.Job property) accelerators_fully_satisfy() (in module toil.job) acquire() (toil.batchSystems.abstractBatchSystem.ResourcePool method) (toil.batchSystems.abstractBatchSystem.ResourceSet method) (toil.batchSystems.kubernetes.ResourcePool method) (toil.batchSystems.singleMachine.ResourcePool method) (toil.batchSystems.singleMachine.ResourceSet method) acquireNow() (toil.batchSystems.abstractBatchSystem.ResourcePool method) (toil.batchSystems.abstractBatchSystem.ResourceSet method) (toil.batchSystems.kubernetes.ResourcePool method) (toil.batchSystems.singleMachine.ResourcePool method) (toil.batchSystems.singleMachine.ResourceSet method) acquisitionOf() (toil.batchSystems.abstractBatchSystem.ResourcePool method) (toil.batchSystems.abstractBatchSystem.ResourceSet method) (toil.batchSystems.kubernetes.ResourcePool method) (toil.batchSystems.singleMachine.ResourcePool method) (toil.batchSystems.singleMachine.ResourceSet method) AcquisitionTimeoutException add_all_batchsystem_options() (in module toil.batchSystems.options) (in module toil.options.common) add_base_toil_options() (in module toil.common) (in module toil.options.common) add_batch_system_factory() (in module toil.batchSystems.registry) (in module toil.test.batchSystems.batch_system_plugin_test) (in module toil.test.batchSystems.batchSystemTest) add_cwl_options() (in module toil.common) (in module toil.options.cwl) add_injections() (toil.wdl.wdltoil.WDLTaskJob method) add_logging_options() (in module toil.common) (in module toil.options.common) (in module toil.statsAndLogging) (in module toil.utils.toilConfig) (in module toil.utils.toilServer) add_options() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem class method) (toil.batchSystems.awsBatch.AWSBatchBatchSystem class method) (toil.batchSystems.kubernetes.KubernetesBatchSystem class method) (toil.batchSystems.local_support.SingleMachineBatchSystem class method) (toil.batchSystems.mesos.batchSystem.MesosBatchSystem class method) (toil.batchSystems.singleMachine.SingleMachineBatchSystem class method) (toil.batchSystems.slurm.SlurmBatchSystem class method) (toil.leader.AbstractBatchSystem class method) (toil.provisioners.clusterScaler.AbstractBatchSystem class method) (toil.test.batchSystems.batch_system_plugin_test.AbstractBatchSystem class method) (toil.test.batchSystems.batch_system_plugin_test.FakeBatchSystem class method) (toil.test.batchSystems.batchSystemTest.AbstractBatchSystem class method) (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystem class method) (toil.test.provisioners.clusterScalerTest.AbstractBatchSystem class method) (toil.test.src.jobServiceTest.SingleMachineBatchSystem class method) add_paths() (in module toil.wdl.wdltoil) add_prometheus_data_source() (toil.common.ToilMetrics method) (toil.leader.ToilMetrics method) add_provisioner_options() (in module toil.common) (in module toil.provisioners) add_stats_options() (in module toil.utils.toilStats) add_to_action_collection() (in module toil.lib.aws.iam) add_toil_service() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) add_wdl_options() (in module toil.common) (in module toil.options.wdl) addBatchSystemFactory() (in module toil.batchSystems.registry) addChild() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.cwl.cwltoil.Job method) (toil.cwl.cwltoil.SelfJob method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.EncapsulatedJob method) (toil.job.Job method) (toil.job.JobDescription method) (toil.job.ServiceHostJob method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.Job method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.src.workerTest.JobDescription method) (toil.test.utils.utilsTest.Job method) (toil.toilState.JobDescription method) (toil.utils.toilStats.Job method) (toil.utils.toilStatus.JobDescription method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) (toil.worker.JobDescription method) addChildFn() (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.Job method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) addChildJobFn() (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.Job method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) addCompletedJob() (toil.leader.ScalerThread method) (toil.provisioners.clusterScaler.ClusterScaler method) (toil.provisioners.clusterScaler.ScalerThread method) (toil.test.provisioners.clusterScalerTest.ClusterScaler method) (toil.test.provisioners.clusterScalerTest.ScalerThread method) addFile() (toil.leader.AbstractProvisioner.InstanceConfiguration method) (toil.provisioners.abstractProvisioner.AbstractProvisioner.InstanceConfiguration method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner.InstanceConfiguration method) (toil.provisioners.clusterScaler.AbstractProvisioner.InstanceConfiguration method) (toil.provisioners.gceProvisioner.AbstractProvisioner.InstanceConfiguration method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner.InstanceConfiguration method) addFollowOn() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.EncapsulatedJob method) (toil.job.Job method) (toil.job.JobDescription method) (toil.job.ServiceHostJob method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.Job method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.src.workerTest.JobDescription method) (toil.test.utils.utilsTest.Job method) (toil.toilState.JobDescription method) (toil.utils.toilStats.Job method) (toil.utils.toilStatus.JobDescription method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) (toil.worker.JobDescription method) addFollowOnFn() (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.Job method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) addFollowOnJobFn() (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.Job method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) addJob() (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method) addJobShape() (toil.provisioners.clusterScaler.BinPackedFit method) (toil.test.provisioners.clusterScalerTest.BinPackedFit method) addKubernetesLeader() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) addKubernetesServices() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) addKubernetesWorker() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) addManagedNodes() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AWSProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.test.provisioners.aws.awsProvisionerTest.AWSProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) addNodeExporterService() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) addNodes() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AWSProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.provisioners.gceProvisioner.GCEProvisioner method) (toil.test.provisioners.aws.awsProvisionerTest.AWSProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method) addOptions() (in module toil.common) (in module toil.cwl.cwltoil) (in module toil.job) (in module toil.test.batchSystems.batch_system_plugin_test) (in module toil.test.options.options) (in module toil.wdl.wdltoil) addPredecessor() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method)

addRandomFollowOnEdges() (toil.test.src.jobTest.JobTest method) addService() (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.EncapsulatedJob method) (toil.job.Job method) (toil.job.ServiceHostJob method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) addServiceHostJob() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) addSSHRSAKey() (toil.leader.AbstractProvisioner.InstanceConfiguration method) (toil.provisioners.abstractProvisioner.AbstractProvisioner.InstanceConfiguration method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner.InstanceConfiguration method) (toil.provisioners.clusterScaler.AbstractProvisioner.InstanceConfiguration method) (toil.provisioners.gceProvisioner.AbstractProvisioner.InstanceConfiguration method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner.InstanceConfiguration method) addToilOptions() (toil.cwl.cwltoil.Job.Runner static method) (toil.fileStores.abstractFileStore.Job.Runner static method) (toil.fileStores.cachingFileStore.Job.Runner static method) (toil.fileStores.nonCachingFileStore.Job.Runner static method) (toil.job.Job.Runner static method) (toil.jobStores.aws.jobStore.Job.Runner static method) (toil.test.batchSystems.batchSystemTest.Job.Runner static method) (toil.test.jobStores.jobStoreTest.Job.Runner static method) (toil.test.lib.dockerTest.Job.Runner static method) (toil.test.mesos.helloWorld.Job.Runner static method) (toil.test.mesos.stress.Job.Runner static method) (toil.test.provisioners.restartScript.Job.Runner static method) (toil.test.sort.restart_sort.Job.Runner static method) (toil.test.sort.sort.Job.Runner static method) (toil.test.sort.sortTest.Job.Runner static method) (toil.test.src.busTest.Job.Runner static method) (toil.test.src.checkpointTest.Job.Runner static method) (toil.test.src.deferredFunctionTest.Job.Runner static method) (toil.test.src.environmentTest.Job.Runner static method) (toil.test.src.fileStoreTest.Job.Runner static method) (toil.test.src.helloWorldTest.Job.Runner static method) (toil.test.src.importExportFileTest.Job.Runner static method) (toil.test.src.jobDescriptionTest.Job.Runner static method) (toil.test.src.jobEncapsulationTest.Job.Runner static method) (toil.test.src.jobFileStoreTest.Job.Runner static method) (toil.test.src.jobServiceTest.Job.Runner static method) (toil.test.src.jobTest.Job.Runner static method) (toil.test.src.promisedRequirementTest.Job.Runner static method) (toil.test.src.promisesTest.Job.Runner static method) (toil.test.src.realtimeLoggerTest.Job.Runner static method) (toil.test.src.restartDAGTest.Job.Runner static method) (toil.test.src.resumabilityTest.Job.Runner static method) (toil.test.src.retainTempDirTest.Job.Runner static method) (toil.test.src.toilContextManagerTest.Job.Runner static method) (toil.test.src.userDefinedJobArgTypeTest.Job.Runner static method) (toil.test.utils.utilsTest.Job.Runner static method) (toil.utils.toilStats.Job.Runner static method) (toil.wdl.wdltoil.Job.Runner static method) (toil.worker.Job.Runner static method) addUnit() (toil.leader.AbstractProvisioner.InstanceConfiguration method) (toil.provisioners.abstractProvisioner.AbstractProvisioner.InstanceConfiguration method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner.InstanceConfiguration method) (toil.provisioners.clusterScaler.AbstractProvisioner.InstanceConfiguration method) (toil.provisioners.gceProvisioner.AbstractProvisioner.InstanceConfiguration method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner.InstanceConfiguration method) addVolumesService() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) adjustCacheLimit() (toil.fileStores.cachingFileStore.CachingFileStore method) adjustEndingReservationForJob() (in module toil.provisioners.clusterScaler) allocatedCores (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemJobTest attribute) allowed_actions_attached() (in module toil.lib.aws.iam) allowed_actions_group() (in module toil.lib.aws.iam) allowed_actions_roles() (in module toil.lib.aws.iam) allowed_actions_user() (in module toil.lib.aws.iam) AllowedActionCollection (in module toil.lib.aws.iam) allSuccessors() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) AlwaysFail (class in toil.test.src.checkpointTest) AMITest (class in toil.test.lib.test_ec2) annotation_name (toil.bus.JobAnnotationMessage attribute) annotation_value (toil.bus.JobAnnotationMessage attribute) annotations (toil.bus.JobStatus attribute) (toil.server.wes.amazon_wes_utils.JobStatus attribute) (toil.server.wes.toil_backend.JobStatus attribute) api (toil.batchSystems.abstractGridEngineBatchSystem.AcceleratorRequirement attribute) (toil.batchSystems.htcondor.AcceleratorRequirement attribute) (toil.batchSystems.singleMachine.AcceleratorRequirement attribute) (toil.cwl.cwltoil.AcceleratorRequirement attribute) (toil.job.AcceleratorRequirement attribute) (toil.lib.accelerators.AcceleratorRequirement attribute) (toil.wdl.wdltoil.AcceleratorRequirement attribute) apiDockerCall() (in module toil.lib.docker) (in module toil.test.lib.dockerTest) ApplianceImageNotFound, [1] applianceSelf() (in module toil) (in module toil.batchSystems.awsBatch) (in module toil.batchSystems.kubernetes) (in module toil.provisioners.abstractProvisioner) (in module toil.test) (in module toil.utils.toilLaunchCluster) ApplianceTestSupport (class in toil.test) (class in toil.test.src.autoDeploymentTest) ApplianceTestSupport.Appliance (class in toil.test) (class in toil.test.src.autoDeploymentTest) ApplianceTestSupport.LeaderThread (class in toil.test) (class in toil.test.src.autoDeploymentTest) ApplianceTestSupport.WorkerThread (class in toil.test) (class in toil.test.src.autoDeploymentTest) apply() (toil.batchSystems.kubernetes.KubernetesBatchSystem.Placement method) apply_bparams() (in module toil.batchSystems.lsfHelper) apply_conf_file() (in module toil.batchSystems.lsfHelper) apply_lsadmin() (in module toil.batchSystems.lsfHelper) aRepr (in module toil.jobStores.aws.jobStore) as_process() (toil.fileStores.cachingFileStore.CachingFileStore method) assert_is_not_newer_than() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) assertIsCopy() (toil.test.src.userDefinedJobArgTypeTest.Foo method) assertUrl() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) assign_job_id() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) assignConfig() (toil.batchSystems.abstractBatchSystem.Requirer method) (toil.batchSystems.awsBatch.Requirer method) (toil.batchSystems.kubernetes.Requirer method) (toil.batchSystems.singleMachine.Requirer method) (toil.batchSystems.slurm.Requirer method) (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.Job method) (toil.job.Requirer method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.batchSystems.batchSystemTest.Requirer method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) assignID() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) assume_zero_overhead (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) atomic_copy() (in module toil.fileStores.cachingFileStore) (in module toil.jobStores.fileJobStore) (in module toil.lib.io) atomic_copyobj() (in module toil.fileStores.cachingFileStore) (in module toil.jobStores.fileJobStore) (in module toil.lib.io) atomic_install() (in module toil.lib.io) (in module toil.test.src.miscTests) atomic_tmp_file() (in module toil.lib.io) (in module toil.test.src.miscTests) AtomicFileCreate() (in module toil.common) (in module toil.jobStores.aws.jobStore) (in module toil.jobStores.fileJobStore) (in module toil.jobStores.googleJobStore) (in module toil.lib.io) (in module toil.server.utils) (in module toil.server.wes.toil_backend) (in module toil.test.src.miscTests) attach_body() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) attemptToAddJob() (toil.provisioners.clusterScaler.NodeReservation method) (toil.test.provisioners.clusterScalerTest.NodeReservation method) attributeDictToList() (toil.jobStores.aws.jobStore.SDBHelper class method) (toil.jobStores.aws.utils.SDBHelper class method) attributeListToDict() (toil.jobStores.aws.jobStore.SDBHelper class method) (toil.jobStores.aws.utils.SDBHelper class method) attributesToBinary() (toil.jobStores.aws.jobStore.SDBHelper class method) (toil.jobStores.aws.utils.SDBHelper class method) AutoDeploymentTest (class in toil.test.src.autoDeploymentTest) aws_batch_batch_system_factory() (in module toil.batchSystems.registry) aws_batch_job_role_arn (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) aws_batch_queue (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) aws_batch_region (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) aws_marketplace_flatcar_ami_search() (in module toil.lib.aws.ami) (in module toil.test.lib.test_ec2) AWSAutoscaleTest (class in toil.test.provisioners.aws.awsProvisionerTest) AWSAutoscaleTestMultipleNodeTypes (class in toil.test.provisioners.aws.awsProvisionerTest) AWSBatchBatchSystem (class in toil.batchSystems.awsBatch) AWSBatchBatchSystemTest (class in toil.test.batchSystems.batchSystemTest) AWSConnectionManager (class in toil.lib.aws.session) (class in toil.provisioners.aws.awsProvisioner) (class in toil.test.provisioners.clusterTest) awsFilterImpairedNodes() (in module toil.provisioners.aws.awsProvisioner) AWSJobStore (class in toil.jobStores.aws.jobStore) (class in toil.test.lib.aws.test_s3) AWSJobStore.FileInfo (class in toil.jobStores.aws.jobStore) (class in toil.test.lib.aws.test_s3) AWSJobStoreTest (class in toil.test.jobStores.jobStoreTest) AWSManagedAutoscaleTest (class in toil.test.provisioners.aws.awsProvisionerTest) AWSProvisioner (class in toil.provisioners.aws.awsProvisioner) (class in toil.test.provisioners.aws.awsProvisionerTest) AWSProvisionerBenchTest (class in toil.test.provisioners.aws.awsProvisionerTest) awsRegion() (toil.test.batchSystems.batch_system_plugin_test.ToilTest class method) (toil.test.batchSystems.batchSystemTest.ToilTest class method) (toil.test.batchSystems.test_lsf_helper.ToilTest class method) (toil.test.batchSystems.test_slurm.ToilTest class method) (toil.test.cwl.cwlTest.ToilTest class method) (toil.test.docs.scriptsTest.ToilTest class method) (toil.test.jobStores.jobStoreTest.ToilTest class method) (toil.test.lib.aws.test_iam.ToilTest class method) (toil.test.lib.aws.test_s3.ToilTest class method) (toil.test.lib.aws.test_utils.ToilTest class method) (toil.test.lib.dockerTest.ToilTest class method) (toil.test.lib.test_conversions.ToilTest class method) (toil.test.lib.test_ec2.ToilTest class method) (toil.test.lib.test_misc.ToilTest class method) (toil.test.mesos.MesosDataStructuresTest.ToilTest class method) (toil.test.options.options.ToilTest class method) (toil.test.provisioners.aws.awsProvisionerTest.ToilTest class method) (toil.test.provisioners.clusterScalerTest.ToilTest class method) (toil.test.provisioners.clusterTest.ToilTest class method) (toil.test.provisioners.gceProvisionerTest.ToilTest class method) (toil.test.provisioners.provisionerTest.ToilTest class method) (toil.test.server.serverTest.ToilTest class method) (toil.test.sort.sortTest.ToilTest class method) (toil.test.src.busTest.ToilTest class method) (toil.test.src.checkpointTest.ToilTest class method) (toil.test.src.deferredFunctionTest.ToilTest class method) (toil.test.src.dockerCheckTest.ToilTest class method) (toil.test.src.environmentTest.ToilTest class method) (toil.test.src.fileStoreTest.ToilTest class method) (toil.test.src.helloWorldTest.ToilTest class method) (toil.test.src.importExportFileTest.ToilTest class method) (toil.test.src.jobDescriptionTest.ToilTest class method) (toil.test.src.jobEncapsulationTest.ToilTest class method) (toil.test.src.jobFileStoreTest.ToilTest class method) (toil.test.src.jobServiceTest.ToilTest class method) (toil.test.src.jobTest.ToilTest class method) (toil.test.src.miscTests.ToilTest class method) (toil.test.src.promisesTest.ToilTest class method) (toil.test.src.realtimeLoggerTest.ToilTest class method) (toil.test.src.regularLogTest.ToilTest class method) (toil.test.src.resourceTest.ToilTest class method) (toil.test.src.restartDAGTest.ToilTest class method) (toil.test.src.resumabilityTest.ToilTest class method) (toil.test.src.retainTempDirTest.ToilTest class method) (toil.test.src.systemTest.ToilTest class method) (toil.test.src.threadingTest.ToilTest class method) (toil.test.src.toilContextManagerTest.ToilTest class method) (toil.test.src.userDefinedJobArgTypeTest.ToilTest class method) (toil.test.src.workerTest.ToilTest class method) (toil.test.ToilTest class method) (toil.test.utils.toilDebugTest.ToilTest class method) (toil.test.utils.toilKillTest.ToilTest class method) (toil.test.utils.utilsTest.ToilTest class method) (toil.test.wdl.wdltoil_test.ToilTest class method) AWSRegionName (in module toil.lib.aws) (in module toil.lib.aws.utils) (in module toil.provisioners.aws.awsProvisioner) AWSRestartTest (class in toil.test.provisioners.aws.awsProvisionerTest) awsRetry() (in module toil.provisioners.aws.awsProvisioner) awsRetryPredicate() (in module toil.provisioners.aws.awsProvisioner) AWSServerErrors (in module toil.jobStores.aws.utils) (in module toil.lib.aws) (in module toil.lib.aws.utils) (in module toil.provisioners.aws.awsProvisioner) AWSStateStoreTest (class in toil.test.server.serverTest) AWSStaticAutoscaleTest (class in toil.test.provisioners.aws.awsProvisionerTest)

B

b() (in module toil.test.src.promisesTest) b2h() (in module toil.lib.humanize) b_to_mib() (in module toil.batchSystems.awsBatch) (in module toil.batchSystems.mesos.batchSystem) (in module toil.lib.conversions) badChild() (in module toil.test.src.resumabilityTest) badWorker (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) badWorkerFailInterval (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) baseVersion (in module toil.options.cwl) (in module toil.server.wes.toil_backend) (in module toil.version) BaseWDLTest (class in toil.test.wdl.wdltoil_test) batch() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) batch_logs_dir (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) batch_system (toil.batchSystems.abstractGridEngineBatchSystem.ExternalBatchIdMessage attribute) (toil.batchSystems.awsBatch.ExternalBatchIdMessage attribute) (toil.batchSystems.singleMachine.ExternalBatchIdMessage attribute) (toil.bus.ExternalBatchIdMessage attribute) (toil.bus.JobStatus attribute) (toil.server.wes.amazon_wes_utils.JobStatus attribute) (toil.server.wes.toil_backend.JobStatus attribute) BatchJobExitReason (class in toil.batchSystems.abstractBatchSystem) (class in toil.batchSystems.abstractGridEngineBatchSystem) (class in toil.batchSystems.awsBatch) (class in toil.batchSystems.kubernetes) (class in toil.batchSystems.lsf) (class in toil.batchSystems.mesos.batchSystem) (class in toil.batchSystems.slurm) (class in toil.leader) (class in toil.test.batchSystems.test_slurm) (class in toil.test.src.busTest) batchSystem (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute)

BatchSystemCleanupSupport (class in toil.batchSystems.abstractGridEngineBatchSystem) (class in toil.batchSystems.awsBatch) (class in toil.batchSystems.cleanup_support) (class in toil.batchSystems.kubernetes) (class in toil.test.batchSystems.batch_system_plugin_test) BatchSystemLocalSupport (class in toil.batchSystems.cleanup_support) (class in toil.batchSystems.local_support) (class in toil.batchSystems.mesos.batchSystem) BatchSystemPluginTest (class in toil.test.batchSystems.batch_system_plugin_test) (class in toil.test.batchSystems.batchSystemTest) BatchSystemSupport (class in toil.batchSystems.abstractBatchSystem) (class in toil.batchSystems.cleanup_support) (class in toil.batchSystems.local_support) (class in toil.batchSystems.mesos.executor) (class in toil.batchSystems.singleMachine) (class in toil.test.batchSystems.batchSystemTest) belongsToToil (toil.deferred.ModuleDescriptor property) (toil.job.ModuleDescriptor property) (toil.resource.ModuleDescriptor property) (toil.test.src.jobDescriptionTest.ModuleDescriptor property) (toil.test.src.resourceTest.ModuleDescriptor property) betaInertia (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) BINARY_PREFIXES (in module toil.lib.conversions) binaryToAttributes() (toil.jobStores.aws.jobStore.SDBHelper class method) (toil.jobStores.aws.utils.SDBHelper class method) binPack() (toil.provisioners.clusterScaler.BinPackedFit method) (toil.test.provisioners.clusterScalerTest.BinPackedFit method) BinPackedFit (class in toil.provisioners.clusterScaler) (class in toil.test.provisioners.clusterScalerTest) binPacking() (in module toil.provisioners.clusterScaler) BinPackingTest (class in toil.test.provisioners.clusterScalerTest) boto3_pager() (in module toil.jobStores.aws.jobStore) (in module toil.lib.aws.utils) (in module toil.provisioners.aws.awsProvisioner) boto3_session (in module toil.jobStores.aws.jobStore) botocore (in module toil.lib.retry) brand (toil.batchSystems.abstractGridEngineBatchSystem.AcceleratorRequirement attribute) (toil.batchSystems.htcondor.AcceleratorRequirement attribute) (toil.batchSystems.singleMachine.AcceleratorRequirement attribute) (toil.cwl.cwltoil.AcceleratorRequirement attribute) (toil.job.AcceleratorRequirement attribute) (toil.lib.accelerators.AcceleratorRequirement attribute) (toil.wdl.wdltoil.AcceleratorRequirement attribute) bucket (toil.test.lib.aws.test_s3.S3Test attribute) (toil.test.server.serverTest.BucketUsingTest attribute) bucket_location_to_region() (in module toil.lib.aws.utils) bucket_name (toil.test.server.serverTest.BucketUsingTest attribute) bucket_path (toil.test.server.serverTest.AWSStateStoreTest attribute) BucketLocationConflictException bucketNameRe (toil.jobStores.aws.jobStore.AWSJobStore attribute) (toil.test.lib.aws.test_s3.AWSJobStore attribute) BucketUsingTest (class in toil.test.server.serverTest) BUFFER_SIZE (toil.cwl.cwltoil.FileJobStore attribute) (toil.jobStores.fileJobStore.FileJobStore attribute) (toil.test.jobStores.jobStoreTest.FileJobStore attribute) (toil.test.src.workerTest.FileJobStore attribute) (toil.utils.toilDebugFile.FileJobStore attribute) (toil.utils.toilDebugJob.FileJobStore attribute) build_element() (in module toil.utils.toilStats) build_tag_dict_from_env() (in module toil.jobStores.aws.jobStore) (in module toil.lib.aws) (in module toil.test.lib.aws.test_utils) (in module toil.utils.toilLaunchCluster) build_wes_request() (toil.server.cli.wes_cwl_runner.WESClientWithWorkflowEngineParameters method) buildLocator() (toil.batchSystems.abstractBatchSystem.Toil static method) (toil.batchSystems.awsBatch.Toil static method) (toil.batchSystems.cleanup_support.Toil static method) (toil.batchSystems.kubernetes.Toil static method) (toil.batchSystems.singleMachine.Toil static method) (toil.common.Toil static method) (toil.cwl.cwltoil.Toil static method) (toil.fileStores.abstractFileStore.Toil static method) (toil.job.Toil static method) (toil.server.wes.tasks.Toil static method) (toil.test.batchSystems.batch_system_plugin_test.Toil static method) (toil.test.batchSystems.batchSystemTest.Toil static method) (toil.test.jobStores.jobStoreTest.Toil static method) (toil.test.lib.dockerTest.Toil static method) (toil.test.mesos.helloWorld.Toil static method) (toil.test.options.options.Toil static method) (toil.test.sort.restart_sort.Toil static method) (toil.test.sort.sort.Toil static method) (toil.test.sort.sortTest.Toil static method) (toil.test.src.busTest.Toil static method) (toil.test.src.environmentTest.Toil static method) (toil.test.src.fileStoreTest.Toil static method) (toil.test.src.importExportFileTest.Toil static method) (toil.test.src.jobDescriptionTest.Toil static method) (toil.test.src.jobFileStoreTest.Toil static method) (toil.test.src.jobTest.Toil static method) (toil.test.src.restartDAGTest.Toil static method) (toil.test.src.toilContextManagerTest.Toil static method) (toil.test.utils.toilKillTest.Toil static method) (toil.test.utils.utilsTest.Toil static method) (toil.utils.toilClean.Toil static method) (toil.utils.toilDebugFile.Toil static method) (toil.utils.toilDebugJob.Toil static method) (toil.utils.toilKill.Toil static method) (toil.utils.toilStats.Toil static method) (toil.utils.toilStatus.Toil static method) (toil.wdl.wdltoil.Toil static method) (toil.worker.Toil static method) bytes2human() (in module toil.fileStores.abstractFileStore) (in module toil.job) (in module toil.lib.conversions) (in module toil.lib.humanize) (in module toil.options.common) (in module toil.provisioners.clusterScaler) bytes_in_unit() (in module toil.lib.conversions) bytes_to_message() (in module toil.bus)

C

c() (in module toil.test.src.promisesTest) c4_8xlarge (in module toil.test.provisioners.clusterScalerTest) c4_8xlarge_preemptible (in module toil.test.provisioners.clusterScalerTest) cache_path (in module toil) cacheDirName() (in module toil.batchSystems.abstractBatchSystem) (in module toil.common) (in module toil.fileStores.abstractFileStore) (in module toil.fileStores.cachingFileStore) CachedUnpicklingJobStoreTest (class in toil.test.src.promisesTest) CacheError cacheTag (in module toil.version) CacheUnbalancedError, [1] caching (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) CachingFileStore (class in toil.fileStores.cachingFileStore) CachingFileStoreTestWithAwsJobStore (class in toil.test.src.fileStoreTest) CachingFileStoreTestWithFileJobStore (class in toil.test.src.fileStoreTest) CachingFileStoreTestWithGoogleJobStore (class in toil.test.src.fileStoreTest) cachingIsFree() (toil.fileStores.cachingFileStore.CachingFileStore method) CactusIntegrationTest (class in toil.test.cactus.test_cactus_integration) call_cmd() (toil.server.wes.tasks.ToilWorkflowRunner method) call_command() (in module toil.batchSystems.gridengine) (in module toil.batchSystems.lsf) (in module toil.batchSystems.slurm) (in module toil.batchSystems.torque) (in module toil.lib.misc) (in module toil.test.src.miscTests) call_sacct() (in module toil.test.batchSystems.test_slurm) call_sacct_raises() (in module toil.test.batchSystems.test_slurm) call_scontrol() (in module toil.test.batchSystems.test_slurm) CalledProcessErrorStderr, [1], [2], [3], [4], [5], [6] can_fake_root() (toil.wdl.wdltoil.WDLTaskJob method) can_mount_proc() (toil.wdl.wdltoil.WDLTaskJob method) cancel() (toil.server.wes.tasks.MultiprocessingTaskRunner class method) (toil.server.wes.tasks.TaskRunner static method) (toil.server.wes.toil_backend.MultiprocessingTaskRunner class method) (toil.server.wes.toil_backend.TaskRunner static method) cancel_run() (in module toil.server.wes.tasks) (toil.server.app.ToilBackend method) (toil.server.wes.abstract_backend.WESBackend method) (toil.server.wes.toil_backend.ToilBackend method) (toil.server.wes.toil_backend.WESBackend method) CATEGORIES (in module toil.utils.toilStats) CATEGORY_UNITS (in module toil.utils.toilStats) celery (in module toil.server.celery_app) (in module toil.server.wes.tasks) cgcloudVersion (in module toil.version) ChainedIndexedPromisesTest (class in toil.test.src.promisesTest) chaining_parent() (in module toil.test.src.resumabilityTest) check() (toil.batchSystems.abstractBatchSystem.MessageBus method) (toil.bus.MessageBus method) (toil.common.MessageBus method) (toil.cwl.cwltoil.Job.Service method) (toil.exceptions.StatsAndLogging method) (toil.fileStores.abstractFileStore.Job.Service method) (toil.fileStores.cachingFileStore.Job.Service method) (toil.fileStores.nonCachingFileStore.Job.Service method) (toil.job.Job.Service method) (toil.jobStores.aws.jobStore.Job.Service method) (toil.leader.ScalerThread method) (toil.leader.ServiceManager method) (toil.leader.StatsAndLogging method) (toil.provisioners.clusterScaler.ScalerThread method) (toil.serviceManager.ServiceManager method) (toil.statsAndLogging.StatsAndLogging method) (toil.test.batchSystems.batchSystemTest.Job.Service method) (toil.test.batchSystems.batchSystemTest.Service method) (toil.test.jobStores.jobStoreTest.Job.Service method) (toil.test.jobStores.jobStoreTest.StatsAndLogging method) (toil.test.lib.dockerTest.Job.Service method) (toil.test.mesos.helloWorld.Job.Service method) (toil.test.mesos.stress.Job.Service method) (toil.test.provisioners.clusterScalerTest.ScalerThread method) (toil.test.provisioners.restartScript.Job.Service method) (toil.test.sort.restart_sort.Job.Service method) (toil.test.sort.sort.Job.Service method) (toil.test.sort.sortTest.Job.Service method) (toil.test.src.busTest.Job.Service method) (toil.test.src.busTest.MessageBus method) (toil.test.src.checkpointTest.Job.Service method) (toil.test.src.deferredFunctionTest.Job.Service method) (toil.test.src.environmentTest.Job.Service method) (toil.test.src.fileStoreTest.Job.Service method) (toil.test.src.helloWorldTest.Job.Service method) (toil.test.src.importExportFileTest.Job.Service method) (toil.test.src.jobDescriptionTest.Job.Service method) (toil.test.src.jobEncapsulationTest.Job.Service method) (toil.test.src.jobFileStoreTest.Job.Service method) (toil.test.src.jobServiceTest.Job.Service method) (toil.test.src.jobServiceTest.ToySerializableService method) (toil.test.src.jobServiceTest.ToyService method) (toil.test.src.jobTest.Job.Service method) (toil.test.src.jobTest.TrivialService method) (toil.test.src.promisedRequirementTest.Job.Service method) (toil.test.src.promisesTest.Job.Service method) (toil.test.src.realtimeLoggerTest.Job.Service method) (toil.test.src.restartDAGTest.Job.Service method) (toil.test.src.resumabilityTest.Job.Service method) (toil.test.src.retainTempDirTest.Job.Service method) (toil.test.src.toilContextManagerTest.Job.Service method) (toil.test.src.userDefinedJobArgTypeTest.Job.Service method) (toil.test.utils.utilsTest.Job.Service method) (toil.toilState.MessageBus method) (toil.utils.toilStats.Job.Service method) (toil.utils.toilStatus.StatsAndLogging method) (toil.wdl.wdltoil.Job.Service method) (toil.worker.Job.Service method) check_and_create_config_file() (in module toil.common) check_and_create_default_config_file() (in module toil.common) check_and_create_toil_home_dir() (in module toil.common) check_configuration_consistency() (toil.batchSystems.abstractBatchSystem.Config method) (toil.batchSystems.awsBatch.Config method) (toil.batchSystems.cleanup_support.Config method) (toil.batchSystems.kubernetes.Config method) (toil.batchSystems.local_support.Config method) (toil.batchSystems.singleMachine.Config method) (toil.common.Config method) (toil.job.Config method) (toil.jobStores.abstractJobStore.Config method) (toil.leader.Config method) (toil.provisioners.clusterScaler.Config method) (toil.test.batchSystems.batchSystemTest.Config method) (toil.test.batchSystems.test_slurm.Config method) (toil.test.jobStores.jobStoreTest.Config method) (toil.test.provisioners.clusterScalerTest.Config method) (toil.test.src.workerTest.Config method) (toil.test.utils.utilsTest.Config method) (toil.utils.toilDebugFile.Config method) (toil.utils.toilDebugJob.Config method) (toil.utils.toilKill.Config method) (toil.utils.toilStats.Config method) (toil.utils.toilStatus.Config method) (toil.worker.Config method) check_cwltool_version() (in module toil.cwl) (in module toil.cwl.cwltoil) check_directory_dict_invariants() (in module toil.cwl.cwltoil) check_environment() (in module toil.test.src.environmentTest) check_environment_repeatedly() (in module toil.test.src.environmentTest) check_for_coordination_corruption() (toil.fileStores.nonCachingFileStore.NonCachingFileStore static method) check_for_state_corruption() (toil.fileStores.nonCachingFileStore.NonCachingFileStore method) check_initialized() (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.Job method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) check_lsf_json_output_supported() (in module toil.batchSystems.lsf) (in module toil.batchSystems.lsfHelper) check_on_run() (toil.server.wes.toil_backend.ToilWorkflow method) check_resource_request() (toil.batchSystems.abstractBatchSystem.BatchSystemSupport method) (toil.batchSystems.cleanup_support.BatchSystemSupport method) (toil.batchSystems.local_support.BatchSystemSupport method) (toil.batchSystems.local_support.SingleMachineBatchSystem method) (toil.batchSystems.mesos.executor.BatchSystemSupport method) (toil.batchSystems.singleMachine.BatchSystemSupport method) (toil.batchSystems.singleMachine.SingleMachineBatchSystem method) (toil.test.batchSystems.batchSystemTest.BatchSystemSupport method) (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystem method) (toil.test.src.jobServiceTest.SingleMachineBatchSystem method) check_status() (toil.test.utils.utilsTest.UtilsTest method) check_valid_node_types() (in module toil.provisioners) (in module toil.utils.toilLaunchCluster) checkDockerImageExists() (in module toil) (in module toil.test.src.dockerCheckTest) checkDockerSchema() (in module toil) checkExitCode() (toil.test.docs.scriptsTest.ToilDocumentationTest method) checkExpectedOut() (toil.test.docs.scriptsTest.ToilDocumentationTest 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(toil.job.Job method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) checkJobGraphForDeadlocks() (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.Job method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) checkNewCheckpointsAreLeafVertices() (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.Job method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) checkOnJobs() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.slurm.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.torque.AbstractGridEngineBatchSystem.GridEngineThread method) checkpoint (toil.cwl.cwltoil.Job property) (toil.fileStores.abstractFileStore.Job property) (toil.fileStores.cachingFileStore.Job property) (toil.fileStores.nonCachingFileStore.Job property) (toil.job.Job property) (toil.jobStores.aws.jobStore.Job property) (toil.test.batchSystems.batchSystemTest.Job property) (toil.test.jobStores.jobStoreTest.Job property) (toil.test.lib.dockerTest.Job property) (toil.test.mesos.helloWorld.Job property) (toil.test.mesos.stress.Job property) (toil.test.provisioners.restartScript.Job property) (toil.test.sort.restart_sort.Job property) (toil.test.sort.sort.Job property) (toil.test.sort.sortTest.Job property) (toil.test.src.busTest.Job property) (toil.test.src.checkpointTest.Job property) (toil.test.src.deferredFunctionTest.Job property) (toil.test.src.environmentTest.Job property) (toil.test.src.fileStoreTest.Job property) (toil.test.src.helloWorldTest.Job property) (toil.test.src.importExportFileTest.Job property) (toil.test.src.jobDescriptionTest.Job property) (toil.test.src.jobEncapsulationTest.Job property) (toil.test.src.jobFileStoreTest.Job property) (toil.test.src.jobServiceTest.Job property) (toil.test.src.jobTest.Job property) (toil.test.src.promisedRequirementTest.Job property) (toil.test.src.promisesTest.Job property) (toil.test.src.realtimeLoggerTest.Job property) (toil.test.src.restartDAGTest.Job property) (toil.test.src.resumabilityTest.Job property) (toil.test.src.retainTempDirTest.Job property) (toil.test.src.toilContextManagerTest.Job property) (toil.test.src.userDefinedJobArgTypeTest.Job property) (toil.test.utils.utilsTest.Job property) (toil.utils.toilStats.Job property) (toil.wdl.wdltoil.Job property) (toil.worker.Job property) CheckpointFailsFirstTime (class in toil.test.src.checkpointTest) CheckpointJobDescription (class in toil.job) (class in toil.jobStores.abstractJobStore) (class in toil.leader) (class in toil.test.src.workerTest) (class in toil.toilState) (class in toil.worker) CheckpointTest (class in toil.test.src.checkpointTest) CheckRetryCount (class in toil.test.src.checkpointTest) checkStats() (toil.provisioners.clusterScaler.ClusterStats method) checksum (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo property) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo property) ChecksumError child() (in module toil.test.src.jobTest) (in module toil.test.src.promisesTest) childFn() (in module toil.test.src.helloWorldTest) (in module toil.test.src.toilContextManagerTest) childJob() (in module toil.test.batchSystems.batchSystemTest) childMessage (in module toil.test.mesos.helloWorld) choose_spot_zone() (in module toil.provisioners.aws) clean (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) clean() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) clean_up() (toil.server.wes.toil_backend.ToilWorkflow method) clean_work_dir (toil.batchSystems.abstractBatchSystem.WorkerCleanupInfo attribute) (toil.batchSystems.cleanup_support.WorkerCleanupInfo attribute) cleanCommand (toil.test.utils.utilsTest.UtilsTest property) cleanJobStoreUtil() (toil.test.provisioners.gceProvisionerTest.AbstractGCEAutoscaleTest method) cleanSystem() (toil.batchSystems.abstractBatchSystem.Resource class method) (toil.batchSystems.awsBatch.Resource class method) (toil.batchSystems.contained_executor.Resource class method) (toil.batchSystems.kubernetes.Resource class method) (toil.batchSystems.mesos.executor.Resource class method) (toil.resource.Resource class method) (toil.test.src.resourceTest.Resource class method) cleanUpExternalStores() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test class method) cleanupWorker() (toil.batchSystems.abstractBatchSystem.DeferredFunctionManager class method) (toil.deferred.DeferredFunctionManager class method) (toil.worker.DeferredFunctionManager class method) cleanWorkDir (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) CleanWorkDirTest (class in toil.test.src.retainTempDirTest) clear_dependents() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) clear_nonexistent_dependents() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) clearRemainingTryCount() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) client() (in module toil.lib.aws.session) (toil.lib.aws.session.AWSConnectionManager method) (toil.provisioners.aws.awsProvisioner.AWSConnectionManager method) (toil.test.provisioners.clusterTest.AWSConnectionManager method) ClientError (in module toil.lib.aws.utils) close() (toil.fileStores.abstractFileStore.WriteWatchingStream method) (toil.jobStores.abstractJobStore.WriteWatchingStream method) (toil.lib.io.WriteWatchingStream method) cloud (toil.leader.AbstractProvisioner attribute) (toil.provisioners.abstractProvisioner.AbstractProvisioner attribute) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner attribute) (toil.provisioners.clusterScaler.AbstractProvisioner attribute) (toil.provisioners.gceProvisioner.AbstractProvisioner attribute) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner attribute) cluster_factory() (in module toil.common) (in module toil.provisioners) (in module toil.test.cactus.test_cactus_integration) (in module toil.test.cwl.cwlTest) (in module toil.test.provisioners.aws.awsProvisionerTest) (in module toil.test.provisioners.clusterTest) (in module toil.test.wdl.wdltoil_test) (in module toil.test.wdl.wdltoil_test_kubernetes) (in module toil.utils.toilDestroyCluster) (in module toil.utils.toilLaunchCluster) (in module toil.utils.toilRsyncCluster) (in module toil.utils.toilSshCluster)

CLUSTER_LAUNCHING_PERMISSIONS (in module toil.lib.aws.iam) (in module toil.provisioners.aws.awsProvisioner) ClusterCombinationNotSupportedException, [1] ClusterDesiredSizeMessage (class in toil.bus) (class in toil.common) (class in toil.provisioners.clusterScaler) ClusterScaler (class in toil.provisioners.clusterScaler) (class in toil.test.provisioners.clusterScalerTest) ClusterScalerTest (class in toil.test.provisioners.clusterScalerTest) ClusterSizeMessage (class in toil.bus) (class in toil.common) (class in toil.provisioners.clusterScaler) ClusterStats (class in toil.provisioners.clusterScaler) clusterStats (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) ClusterTypeNotSupportedException, [1] coalesce_job_exit_codes() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.lsf.LSFBatchSystem.GridEngineThread method) (toil.batchSystems.slurm.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.slurm.SlurmBatchSystem.GridEngineThread method) (toil.batchSystems.torque.AbstractGridEngineBatchSystem.GridEngineThread method) coalesce_nodes() (toil.test.wdl.wdltoil_test.WDLSectionJob static method) (toil.wdl.wdltoil.WDLSectionJob static method) coalesceStatusCalls (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) collapse_tags() (in module toil.provisioners.aws.awsProvisioner) collect_attachments() (toil.server.wes.abstract_backend.WESBackend method) (toil.server.wes.toil_backend.WESBackend method) collect_ignore (in module toil.batchSystems.mesos.conftest) (in module toil.cwl.conftest) (in module toil.jobStores.conftest) (in module toil.lib.encryption.conftest) (in module toil.test.cwl.conftest) collect_policy_actions() (in module toil.lib.aws.iam) collect_process_name_garbage() (in module toil.lib.threading) colored_logs (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) ColumnWidths (class in toil.utils.toilStats) combine_bindings() (in module toil.wdl.wdltoil) commit_job() (toil.leader.ToilState method) (toil.serviceManager.ToilState method) (toil.toilState.ToilState method) compat_bytes() (in module toil.jobStores.aws.jobStore) (in module toil.jobStores.aws.utils) (in module toil.jobStores.googleJobStore) (in module toil.lib.compatibility) compat_bytes_recursive() (in module toil.lib.compatibility) (in module toil.provisioners.gceProvisioner) compute_column_widths() (in module toil.utils.toilStats) COMPUTED_CATEGORIES (in module toil.utils.toilStats) con (toil.fileStores.cachingFileStore.CachingFileStore property) concat (class in toil.lib.iterables) (class in toil.resource) (class in toil.test) (class in toil.test.src.autoDeploymentTest) ConcurrentFileModificationException, [1] Conditional (class in toil.cwl.cwltoil) Config (class in toil.batchSystems.abstractBatchSystem) (class in toil.batchSystems.awsBatch) (class in toil.batchSystems.cleanup_support) (class in toil.batchSystems.kubernetes) (class in toil.batchSystems.local_support) (class in toil.batchSystems.singleMachine) (class in toil.common) (class in toil.job) (class in toil.jobStores.abstractJobStore) (class in toil.leader) (class in toil.provisioners.clusterScaler) (class in toil.test.batchSystems.batchSystemTest) (class in toil.test.batchSystems.test_slurm) (class in toil.test.jobStores.jobStoreTest) (class in toil.test.provisioners.clusterScalerTest) (class in toil.test.src.workerTest) (class in toil.test.utils.utilsTest) (class in toil.utils.toilDebugFile) (class in toil.utils.toilDebugJob) (class in toil.utils.toilKill) (class in toil.utils.toilStats) (class in toil.utils.toilStatus) (class in toil.worker) config (toil.batchSystems.abstractBatchSystem.Toil attribute) (toil.batchSystems.awsBatch.Toil attribute) (toil.batchSystems.cleanup_support.Toil attribute) (toil.batchSystems.kubernetes.Toil attribute) (toil.batchSystems.singleMachine.Toil attribute) (toil.common.Toil attribute) (toil.cwl.cwltoil.AbstractJobStore property) (toil.cwl.cwltoil.Toil attribute) (toil.cwl.utils.AbstractJobStore property) (toil.fileStores.abstractFileStore.AbstractJobStore property) (toil.fileStores.abstractFileStore.Toil attribute) (toil.fileStores.cachingFileStore.AbstractJobStore property) (toil.fileStores.nonCachingFileStore.AbstractJobStore property) (toil.job.Toil attribute) (toil.jobStores.abstractJobStore.AbstractJobStore property) (toil.jobStores.aws.jobStore.AbstractJobStore property) (toil.jobStores.fileJobStore.AbstractJobStore property) (toil.jobStores.googleJobStore.AbstractJobStore property) (toil.leader.AbstractJobStore property) (toil.server.wes.tasks.Toil attribute) (toil.serviceManager.AbstractJobStore property) (toil.test.batchSystems.batch_system_plugin_test.Toil attribute) (toil.test.batchSystems.batchSystemTest.Toil attribute) (toil.test.jobStores.jobStoreTest.Toil attribute) (toil.test.lib.dockerTest.Toil attribute) (toil.test.mesos.helloWorld.Toil attribute) (toil.test.options.options.Toil attribute) (toil.test.sort.restart_sort.Toil attribute) (toil.test.sort.sort.Toil attribute) (toil.test.sort.sortTest.Toil attribute) (toil.test.src.busTest.Toil attribute) (toil.test.src.environmentTest.Toil attribute) (toil.test.src.fileStoreTest.Toil attribute) (toil.test.src.importExportFileTest.Toil attribute) (toil.test.src.jobDescriptionTest.Toil attribute) (toil.test.src.jobFileStoreTest.Toil attribute) (toil.test.src.jobTest.Toil attribute) (toil.test.src.restartDAGTest.Toil attribute) (toil.test.src.toilContextManagerTest.Toil attribute) (toil.test.utils.toilKillTest.Toil attribute) (toil.test.utils.utilsTest.Toil attribute) (toil.toilState.AbstractJobStore property) (toil.utils.toilClean.Toil attribute) (toil.utils.toilDebugFile.Toil attribute) (toil.utils.toilDebugJob.Toil attribute) (toil.utils.toilKill.Toil attribute) (toil.utils.toilStats.AbstractJobStore property) (toil.utils.toilStats.Toil attribute) (toil.utils.toilStatus.Toil attribute) (toil.wdl.wdltoil.AbstractJobStore property) (toil.wdl.wdltoil.Toil attribute) (toil.worker.AbstractJobStore property) (toil.worker.Toil attribute) configure_root_logger() (in module toil.batchSystems.contained_executor) (in module toil.batchSystems.mesos.executor) (in module toil.statsAndLogging) (in module toil.worker) ConflictingPredecessorError CONFORMANCE_TEST_TIMEOUT (in module toil.test.cwl.cwlTest) connect() (toil.batchSystems.abstractBatchSystem.MessageBus method) (toil.bus.MessageBus method) (toil.common.MessageBus method) (toil.test.src.busTest.MessageBus method) (toil.toilState.MessageBus method) connect_output_file() (toil.batchSystems.abstractBatchSystem.MessageBus method) (toil.bus.MessageBus method) (toil.common.MessageBus method) (toil.test.src.busTest.MessageBus method) (toil.toilState.MessageBus method) connect_to_state_store() (in module toil.server.utils) connect_to_workflow_state_store() (in module toil.server.utils) (in module toil.server.wes.tasks) (in module toil.server.wes.toil_backend) connect_toil_job() (toil.cwl.cwltoil.ToilTool method) connection_error() (in module toil.jobStores.aws.utils) (in module toil.lib.aws.utils) connection_reset() (in module toil.lib.aws.utils) connectSchedd() (toil.batchSystems.htcondor.HTCondorBatchSystem.GridEngineThread method) CONSISTENCY_TICKS (in module toil.jobStores.aws.jobStore) CONSISTENCY_TIME (in module toil.jobStores.aws.jobStore) containerIsRunning() (in module toil.lib.docker) (in module toil.test.lib.dockerTest) content (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo property) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo property) ConversionTest (class in toil.test.lib.test_conversions) convert_units() (in module toil.batchSystems.lsfHelper) (in module toil.lib.conversions) (in module toil.test.lib.test_conversions) (in module toil.wdl.wdltoil) convertPromises() (toil.job.PromisedRequirement static method) (toil.test.src.promisedRequirementTest.PromisedRequirement static method) coordination_dir (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.abstractBatchSystem.WorkerCleanupInfo attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.cleanup_support.WorkerCleanupInfo attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) copy() (toil.batchSystems.mesos.executor.Expando method) (toil.job.Expando method) (toil.lib.expando.Expando method) (toil.statsAndLogging.Expando method) (toil.utils.toilStats.Expando method) copyFrom() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo method) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo method) copyKeyMultipart() (in module toil.jobStores.aws.jobStore) (in module toil.jobStores.aws.utils) copySshKeys() (toil.provisioners.abstractProvisioner.Node method) (toil.provisioners.aws.awsProvisioner.Node method) (toil.provisioners.gceProvisioner.Node method) (toil.provisioners.node.Node method) (toil.test.provisioners.clusterScalerTest.Node method) copySubRangeOfFile() (in module toil.test.sort.restart_sort) (in module toil.test.sort.sort) (in module toil.test.sort.sortTest) copyTo() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo method) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo method) coreRsync() (toil.provisioners.abstractProvisioner.Node method) (toil.provisioners.aws.awsProvisioner.Node method) (toil.provisioners.gceProvisioner.Node method) (toil.provisioners.node.Node method) (toil.test.provisioners.clusterScalerTest.Node method) cores (toil.batchSystems.abstractBatchSystem.Requirer property) (toil.batchSystems.awsBatch.Requirer property) (toil.batchSystems.kubernetes.Requirer property) (toil.batchSystems.singleMachine.Requirer property) (toil.batchSystems.slurm.Requirer property) (toil.cwl.cwltoil.Job property) (toil.fileStores.abstractFileStore.Job property) (toil.fileStores.cachingFileStore.Job property) (toil.fileStores.nonCachingFileStore.Job property) (toil.job.Job property) (toil.job.RequirementsDict attribute) (toil.job.Requirer property) (toil.jobStores.aws.jobStore.Job property) (toil.test.batchSystems.batchSystemTest.Job property) (toil.test.batchSystems.batchSystemTest.Requirer property) (toil.test.jobStores.jobStoreTest.Job property) (toil.test.lib.dockerTest.Job property) (toil.test.mesos.helloWorld.Job property) (toil.test.mesos.stress.Job property) (toil.test.provisioners.restartScript.Job property) (toil.test.sort.restart_sort.Job property) (toil.test.sort.sort.Job property) (toil.test.sort.sortTest.Job property) (toil.test.src.busTest.Job property) (toil.test.src.checkpointTest.Job property) (toil.test.src.deferredFunctionTest.Job property) (toil.test.src.environmentTest.Job property) (toil.test.src.fileStoreTest.Job property) (toil.test.src.helloWorldTest.Job property) (toil.test.src.importExportFileTest.Job property) (toil.test.src.jobDescriptionTest.Job property) (toil.test.src.jobEncapsulationTest.Job property) (toil.test.src.jobFileStoreTest.Job property) (toil.test.src.jobServiceTest.Job property) (toil.test.src.jobTest.Job property) (toil.test.src.promisedRequirementTest.Job property) (toil.test.src.promisesTest.Job property) (toil.test.src.realtimeLoggerTest.Job property) (toil.test.src.restartDAGTest.Job property) (toil.test.src.resumabilityTest.Job property) (toil.test.src.retainTempDirTest.Job property) (toil.test.src.toilContextManagerTest.Job property) (toil.test.src.userDefinedJobArgTypeTest.Job property) (toil.test.utils.utilsTest.Job property) (toil.utils.toilStats.Job property) (toil.wdl.wdltoil.Job property) (toil.worker.Job property) coreSSH() (toil.provisioners.abstractProvisioner.Node method) (toil.provisioners.aws.awsProvisioner.Node method) (toil.provisioners.gceProvisioner.Node method) (toil.provisioners.node.Node method) (toil.test.provisioners.clusterScalerTest.Node method) count (toil.batchSystems.abstractGridEngineBatchSystem.AcceleratorRequirement attribute) (toil.batchSystems.htcondor.AcceleratorRequirement attribute) (toil.batchSystems.singleMachine.AcceleratorRequirement attribute) (toil.cwl.cwltoil.AcceleratorRequirement attribute) (toil.job.AcceleratorRequirement attribute) (toil.lib.accelerators.AcceleratorRequirement attribute) (toil.wdl.wdltoil.AcceleratorRequirement attribute) count() (in module toil.test.batchSystems.batchSystemTest) (toil.bus.MessageInbox method) count_nvidia_gpus() (in module toil.lib.accelerators) count_pending_successors() (toil.leader.ToilState method) (toil.serviceManager.ToilState method) (toil.toilState.ToilState method) CovItemT (toil.batchSystems.kubernetes.KubernetesBatchSystem attribute) cpu_count() (in module toil.batchSystems.local_support) (in module toil.batchSystems.mesos.executor) (in module toil.batchSystems.mesos.test) (in module toil.batchSystems.options) (in module toil.batchSystems.singleMachine) (in module toil.lib.threading) (in module toil.test) (in module toil.test.batchSystems.batchSystemTest) (in module toil.test.cwl.cwlTest) (in module toil.test.src.deferredFunctionTest) (in module toil.test.src.systemTest) (in module toil.test.src.threadingTest) cpuCount (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemJobTest attribute) create() (toil.batchSystems.abstractBatchSystem.Resource class method) (toil.batchSystems.awsBatch.Resource class method) (toil.batchSystems.contained_executor.Resource class method) (toil.batchSystems.kubernetes.Resource class method) (toil.batchSystems.mesos.executor.Resource class method) (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.deferred.DeferredFunction class method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.job.DeferredFunction class method) (toil.job.PromisedRequirementFunctionWrappingJob class method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo class method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.resource.Resource class method) (toil.serviceManager.AbstractJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo class method) (toil.test.src.resourceTest.Resource class method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) create_app() (in module toil.server.app) create_auto_scaling_group() (in module toil.lib.ec2) (in module toil.provisioners.aws.awsProvisioner) create_celery_app() (in module toil.server.celery_app) create_client() (toil.jobStores.googleJobStore.GoogleJobStore class method) (toil.provisioners.gceProvisioner.GoogleJobStore class method) create_file() (toil.test.src.fileStoreTest.hidden.AbstractFileStoreTest method) (toil.test.src.importExportFileTest.ImportExportFileTest method) create_instances() (in module toil.lib.ec2) (in module toil.provisioners.aws.awsProvisioner) create_job() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) create_launch_template() (in module toil.lib.ec2) (in module toil.provisioners.aws.awsProvisioner) create_ondemand_instances() (in module toil.lib.ec2) (in module toil.provisioners.aws.awsProvisioner) create_root_job() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) create_s3_bucket() (in module toil.jobStores.aws.jobStore) (in module toil.lib.aws.utils) (in module toil.provisioners.aws.awsProvisioner) (in module toil.test.lib.aws.test_s3) create_spot_instances() (in module toil.lib.ec2) (in module toil.provisioners.aws.awsProvisioner) create_status_sentinel_file() (toil.leader.Leader method) create_subgraph() (toil.test.wdl.wdltoil_test.WDLSectionJob method) (toil.wdl.wdltoil.WDLSectionJob method) create_summary() (in module toil.utils.toilStats) create_tags_dict() (in module toil.utils.toilLaunchCluster) createBatchSystem() (toil.batchSystems.abstractBatchSystem.Toil static method) (toil.batchSystems.awsBatch.Toil static method) (toil.batchSystems.cleanup_support.Toil static method) (toil.batchSystems.kubernetes.Toil static method) (toil.batchSystems.singleMachine.Toil static method) (toil.common.Toil static method) (toil.cwl.cwltoil.Toil static method) (toil.fileStores.abstractFileStore.Toil static method) (toil.job.Toil static method) (toil.server.wes.tasks.Toil static method) (toil.test.batchSystems.batch_system_plugin_test.Toil static method) (toil.test.batchSystems.batchSystemTest.AWSBatchBatchSystemTest method) (toil.test.batchSystems.batchSystemTest.GridEngineBatchSystemTest method) (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemTest method) (toil.test.batchSystems.batchSystemTest.HTCondorBatchSystemTest method) (toil.test.batchSystems.batchSystemTest.KubernetesBatchSystemTest method) (toil.test.batchSystems.batchSystemTest.LSFBatchSystemTest method) (toil.test.batchSystems.batchSystemTest.MesosBatchSystemTest method) (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystemTest method) (toil.test.batchSystems.batchSystemTest.SlurmBatchSystemTest method) (toil.test.batchSystems.batchSystemTest.Toil static method) (toil.test.batchSystems.batchSystemTest.TorqueBatchSystemTest method) (toil.test.jobStores.jobStoreTest.Toil static method) (toil.test.lib.dockerTest.Toil static method) (toil.test.mesos.helloWorld.Toil static method) (toil.test.options.options.Toil static method) (toil.test.sort.restart_sort.Toil static method) (toil.test.sort.sort.Toil static method) (toil.test.sort.sortTest.Toil static method) (toil.test.src.busTest.Toil static method) (toil.test.src.environmentTest.Toil static method) (toil.test.src.fileStoreTest.Toil static method) (toil.test.src.importExportFileTest.Toil static method) (toil.test.src.jobDescriptionTest.Toil static method) (toil.test.src.jobFileStoreTest.Toil static method) (toil.test.src.jobTest.Toil static method) (toil.test.src.restartDAGTest.Toil static method) (toil.test.src.toilContextManagerTest.Toil static method) (toil.test.utils.toilKillTest.Toil static method) (toil.test.utils.utilsTest.Toil static method) (toil.utils.toilClean.Toil static method) (toil.utils.toilDebugFile.Toil static method) (toil.utils.toilDebugJob.Toil static method) (toil.utils.toilKill.Toil static method) (toil.utils.toilStats.Toil static method) (toil.utils.toilStatus.Toil static method) (toil.wdl.wdltoil.Toil static method) (toil.worker.Toil static method) createClusterSettings() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AWSProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.provisioners.gceProvisioner.GCEProvisioner method) (toil.test.provisioners.aws.awsProvisionerTest.AWSProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method) createClusterUtil() (toil.test.cactus.test_cactus_integration.AbstractClusterTest method) (toil.test.provisioners.aws.awsProvisionerTest.AbstractClusterTest method) (toil.test.provisioners.clusterTest.AbstractClusterTest method) (toil.test.provisioners.gceProvisionerTest.AbstractGCEAutoscaleTest method) (toil.test.wdl.wdltoil_test_kubernetes.AbstractClusterTest method) createConfig() (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemTest class method) (toil.test.batchSystems.batchSystemTest.MesosBatchSystemTest class method) createFileStore() (toil.batchSystems.abstractBatchSystem.AbstractFileStore static method) (toil.cwl.cwltoil.AbstractFileStore static method) (toil.cwl.utils.AbstractFileStore static method) (toil.fileStores.abstractFileStore.AbstractFileStore static method) (toil.fileStores.cachingFileStore.AbstractFileStore static method) (toil.fileStores.nonCachingFileStore.AbstractFileStore static method) (toil.test.cwl.cwlTest.AbstractFileStore static method) (toil.wdl.wdltoil.AbstractFileStore static method) (toil.worker.AbstractFileStore static method) createJobs() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.htcondor.HTCondorBatchSystem.GridEngineThread method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.slurm.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.torque.AbstractGridEngineBatchSystem.GridEngineThread method) createRootJob() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) cur (toil.fileStores.cachingFileStore.CachingFileStore property) current_process_name_for (in module toil.lib.threading) current_process_name_lock (in module toil.lib.threading) current_size (toil.bus.ClusterSizeMessage attribute) (toil.common.ClusterSizeMessage attribute) (toil.provisioners.clusterScaler.ClusterSizeMessage attribute) currentCommit (in module toil) (in module toil.version) custom_repr (in module toil.jobStores.aws.jobStore) customDockerInitCmd() (in module toil) (in module toil.provisioners.abstractProvisioner) customInitCmd() (in module toil) (in module toil.provisioners.abstractProvisioner) cwl (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) CWL_UNSUPPORTED_REQUIREMENT_EXCEPTION (in module toil.cwl.cwltoil) (in module toil.cwl.utils) (in module toil.worker) CWL_UNSUPPORTED_REQUIREMENT_EXIT_CODE (in module toil.cwl.cwltoil) (in module toil.cwl.utils) (in module toil.leader) (in module toil.worker) CWLGather (class in toil.cwl.cwltoil) CWLJob (class in toil.cwl.cwltoil) CWLJobWrapper (class in toil.cwl.cwltoil) CWLNamedJob (class in toil.cwl.cwltoil) CWLOnARMTest (class in toil.test.provisioners.clusterTest) CWLScatter (class in toil.cwl.cwltoil) cwlSpec (toil.test.cwl.cwlTest.CWLv11Test attribute) (toil.test.cwl.cwlTest.CWLv12Test attribute) cwltoil_was_removed() (in module toil.cwl.cwltoil) cwltool_version (in module toil.cwl) (in module toil.version) CWLUnsupportedException CWLv10Test (class in toil.test.cwl.cwlTest) CWLv11Test (class in toil.test.cwl.cwlTest) CWLv12Test (class in toil.test.cwl.cwlTest) CWLWorkflow (class in toil.cwl.cwltoil) CWLWorkflowTest (class in toil.test.cwl.cwlTest)

D

d() (in module toil.test.src.promisesTest) daddy() (toil.batchSystems.local_support.SingleMachineBatchSystem method) (toil.batchSystems.singleMachine.SingleMachineBatchSystem method) (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystem method) (toil.test.src.jobServiceTest.SingleMachineBatchSystem method) data (toil.server.wes.amazon_wes_utils.WorkflowPlan attribute) data() (toil.test.provisioners.aws.awsProvisionerTest.AbstractAWSAutoscaleTest method) DataDict (class in toil.server.wes.amazon_wes_utils) DataStructuresTest (class in toil.test.mesos.MesosDataStructuresTest) deadlockCheckInterval (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) DeadlockException, [1], [2] deadlockWait (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) DebugJobTest (class in toil.test.utils.toilDebugTest) DebugStoppingPointReached, [1], [2] debugWorker (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) DECIMAL_PREFIXES (in module toil.lib.conversions) decode_directory() (in module toil.cwl.cwltoil) decorate_subheader() (in module toil.utils.toilStats) decorate_title() (in module toil.utils.toilStats) DEFAULT_BATCH_SYSTEM (in module toil.batchSystems.options) (in module toil.batchSystems.registry) (in module toil.cwl.cwltoil) default_caching() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) DEFAULT_CONFIG_FILE (in module toil.common) DEFAULT_DELAYS (in module toil.batchSystems.abstractGridEngineBatchSystem) (in module toil.jobStores.aws.utils) (in module toil.lib.aws.utils) (in module toil.lib.retry) DEFAULT_LOGLEVEL (in module toil.cwl.cwltoil) (in module toil.statsAndLogging) DEFAULT_LSF_UNITS (in module toil.batchSystems.lsfHelper) DEFAULT_RESOURCE_UNITS (in module toil.batchSystems.lsfHelper) DEFAULT_TASK_COMPLETION_TIMEOUT (toil.provisioners.gceProvisioner.GCEProvisioner attribute) DEFAULT_TIMEOUT (in module toil.jobStores.aws.utils) (in module toil.lib.aws.utils) (in module toil.lib.retry) DEFAULT_TMPDIR (in module toil.cwl.cwltoil) DEFAULT_TMPDIR_PREFIX (in module toil.cwl.cwltoil) defaultAccelerators (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) defaultCores (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) defaultDisk (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) defaultLevel (toil.common.RealtimeLogger attribute) (toil.deferred.RealtimeLogger attribute) (toil.realtimeLogger.RealtimeLogger attribute) (toil.test.sort.restart_sort.RealtimeLogger attribute) (toil.test.sort.sort.RealtimeLogger attribute) (toil.test.src.fileStoreTest.RealtimeLogger attribute) (toil.test.src.realtimeLoggerTest.RealtimeLogger attribute) defaultLineLen (in module toil.test.sort.restart_sort) (in module toil.test.sort.sort) (in module toil.test.sort.sortTest) defaultLines (in module toil.test.sort.restart_sort) (in module toil.test.sort.sort) (in module toil.test.sort.sortTest) defaultMemory (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) defaultN (in module toil.test.sort.sortTest) defaultPreemptible (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) defaultRequirements (in module toil.test.batchSystems.batchSystemTest) defaultTargetTime (in module toil.options.common) (in module toil.provisioners.clusterScaler) (in module toil.test.provisioners.clusterScalerTest) DefaultWithSource (class in toil.cwl.cwltoil) defer() (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.Job method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) defer_postprocessing() (toil.wdl.wdltoil.WDLBaseJob method) DeferredFunction (class in toil.deferred) (class in toil.job) DeferredFunctionManager (class in toil.batchSystems.abstractBatchSystem) (class in toil.deferred) (class in toil.worker) DeferredFunctionTest (class in toil.test.src.deferredFunctionTest) delete() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) delete_file() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) delete_iam_instance_profile() (in module toil.lib.aws.utils) delete_iam_role() (in module toil.lib.aws.utils) delete_job() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.leader.ToilState method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.serviceManager.ToilState method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.toilState.ToilState method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) delete_s3_bucket() (in module toil.lib.aws.utils) delete_sdb_domain() (in module toil.lib.aws.utils) deleteFile() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method)

deleteGlobalFile() (toil.batchSystems.abstractBatchSystem.AbstractFileStore method) (toil.cwl.cwltoil.AbstractFileStore method) (toil.cwl.utils.AbstractFileStore method) (toil.fileStores.abstractFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.CachingFileStore method) (toil.fileStores.nonCachingFileStore.AbstractFileStore method) (toil.fileStores.nonCachingFileStore.NonCachingFileStore method) (toil.test.cwl.cwlTest.AbstractFileStore method) (toil.wdl.wdltoil.AbstractFileStore method) (toil.worker.AbstractFileStore method) deleteLocalFile() (toil.batchSystems.abstractBatchSystem.AbstractFileStore method) (toil.cwl.cwltoil.AbstractFileStore method) (toil.cwl.utils.AbstractFileStore method) (toil.fileStores.abstractFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.CachingFileStore method) (toil.fileStores.nonCachingFileStore.AbstractFileStore method) (toil.fileStores.nonCachingFileStore.NonCachingFileStore method) (toil.test.cwl.cwlTest.AbstractFileStore method) (toil.wdl.wdltoil.AbstractFileStore method) (toil.worker.AbstractFileStore method) deployScript() (toil.test.ApplianceTestSupport.Appliance method) (toil.test.src.autoDeploymentTest.ApplianceTestSupport.Appliance method) deprecated() (in module toil.batchSystems.registry) (in module toil.common) (in module toil.fileStores.abstractFileStore) (in module toil.fileStores.cachingFileStore) (in module toil.fileStores.nonCachingFileStore) (in module toil.job) (in module toil.jobStores.abstractJobStore) (in module toil.lib.compatibility) description (toil.cwl.cwltoil.Job property) (toil.fileStores.abstractFileStore.Job property) (toil.fileStores.cachingFileStore.Job property) (toil.fileStores.nonCachingFileStore.Job property) (toil.job.Job property) (toil.jobStores.aws.jobStore.Job property) (toil.test.batchSystems.batchSystemTest.Job property) (toil.test.jobStores.jobStoreTest.Job property) (toil.test.lib.dockerTest.Job property) (toil.test.mesos.helloWorld.Job property) (toil.test.mesos.stress.Job property) (toil.test.provisioners.restartScript.Job property) (toil.test.sort.restart_sort.Job property) (toil.test.sort.sort.Job property) (toil.test.sort.sortTest.Job property) (toil.test.src.busTest.Job property) (toil.test.src.checkpointTest.Job property) (toil.test.src.deferredFunctionTest.Job property) (toil.test.src.environmentTest.Job property) (toil.test.src.fileStoreTest.Job property) (toil.test.src.helloWorldTest.Job property) (toil.test.src.importExportFileTest.Job property) (toil.test.src.jobDescriptionTest.Job property) (toil.test.src.jobEncapsulationTest.Job property) (toil.test.src.jobFileStoreTest.Job property) (toil.test.src.jobServiceTest.Job property) (toil.test.src.jobTest.Job property) (toil.test.src.promisedRequirementTest.Job property) (toil.test.src.promisesTest.Job property) (toil.test.src.realtimeLoggerTest.Job property) (toil.test.src.restartDAGTest.Job property) (toil.test.src.resumabilityTest.Job property) (toil.test.src.retainTempDirTest.Job property) (toil.test.src.toilContextManagerTest.Job property) (toil.test.src.userDefinedJobArgTypeTest.Job property) (toil.test.utils.utilsTest.Job property) (toil.utils.toilStats.Job property) (toil.wdl.wdltoil.Job property) (toil.worker.Job property) desired_labels (toil.batchSystems.kubernetes.KubernetesBatchSystem.Placement attribute) desired_size (toil.bus.ClusterDesiredSizeMessage attribute) (toil.common.ClusterDesiredSizeMessage attribute) (toil.provisioners.clusterScaler.ClusterDesiredSizeMessage attribute) destroy() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) destroy_all_process_names() (in module toil.lib.threading) destroyCluster() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AWSProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.provisioners.gceProvisioner.GCEProvisioner method) (toil.test.cactus.test_cactus_integration.AbstractClusterTest method) (toil.test.provisioners.aws.awsProvisionerTest.AbstractClusterTest method) (toil.test.provisioners.aws.awsProvisionerTest.AWSProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method) (toil.test.provisioners.clusterTest.AbstractClusterTest method) (toil.test.wdl.wdltoil_test_kubernetes.AbstractClusterTest method) destroyClusterUtil() (toil.test.provisioners.gceProvisionerTest.AbstractGCEAutoscaleTest method) detach_body() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) determine_load_listing() (in module toil.cwl.cwltoil) devirtualize_files() (in module toil.wdl.wdltoil) devirtualize_to() (toil.wdl.wdltoil.ToilWDLStdLibBase static method) DIAL_SPECIFIC_REGION_CONFIG (in module toil.jobStores.aws.utils) diamond() (in module toil.test.src.jobTest) DirectoryContents (in module toil.cwl.cwltoil) DirectoryResource (class in toil.resource) DirectoryStructure (in module toil.cwl.utils) (in module toil.test.cwl.cwlTest) dirname (in module toil.lib.ec2nodes) dirPath (toil.deferred.ModuleDescriptor attribute) (toil.job.ModuleDescriptor attribute) (toil.resource.ModuleDescriptor attribute) (toil.test.src.jobDescriptionTest.ModuleDescriptor attribute) (toil.test.src.resourceTest.ModuleDescriptor attribute) dirty (in module toil.version) disableAutoDeployment (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) disableChaining (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) disableJobStoreChecksumVerification (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) disableProgress (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) disableWorkerOutputCapture (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) disconnected() (toil.batchSystems.mesos.executor.MesosExecutor method) disk (toil.batchSystems.abstractBatchSystem.Requirer property) (toil.batchSystems.awsBatch.Requirer property) (toil.batchSystems.kubernetes.Requirer property) (toil.batchSystems.singleMachine.Requirer property) (toil.batchSystems.slurm.Requirer property) (toil.cwl.cwltoil.Job property) (toil.fileStores.abstractFileStore.Job property) (toil.fileStores.cachingFileStore.Job property) (toil.fileStores.nonCachingFileStore.Job property) (toil.job.Job property) (toil.job.RequirementsDict attribute) (toil.job.Requirer property) (toil.jobStores.aws.jobStore.Job property) (toil.test.batchSystems.batchSystemTest.Job property) (toil.test.batchSystems.batchSystemTest.Requirer property) (toil.test.jobStores.jobStoreTest.Job property) (toil.test.lib.dockerTest.Job property) (toil.test.mesos.helloWorld.Job property) (toil.test.mesos.stress.Job property) (toil.test.provisioners.restartScript.Job property) (toil.test.sort.restart_sort.Job property) (toil.test.sort.sort.Job property) (toil.test.sort.sortTest.Job property) (toil.test.src.busTest.Job property) (toil.test.src.checkpointTest.Job property) (toil.test.src.deferredFunctionTest.Job property) (toil.test.src.environmentTest.Job property) (toil.test.src.fileStoreTest.Job property) (toil.test.src.helloWorldTest.Job property) (toil.test.src.importExportFileTest.Job property) (toil.test.src.jobDescriptionTest.Job property) (toil.test.src.jobEncapsulationTest.Job property) (toil.test.src.jobFileStoreTest.Job property) (toil.test.src.jobServiceTest.Job property) (toil.test.src.jobTest.Job property) (toil.test.src.promisedRequirementTest.Job property) (toil.test.src.promisesTest.Job property) (toil.test.src.realtimeLoggerTest.Job property) (toil.test.src.restartDAGTest.Job property) (toil.test.src.resumabilityTest.Job property) (toil.test.src.retainTempDirTest.Job property) (toil.test.src.toilContextManagerTest.Job property) (toil.test.src.userDefinedJobArgTypeTest.Job property) (toil.test.utils.utilsTest.Job property) (toil.utils.toilStats.Job property) (toil.wdl.wdltoil.Job property) (toil.worker.Job property) display_name (toil.bus.Names attribute) (toil.job.Names attribute) distVersion (in module toil.test) (in module toil.version) do_eval() (toil.cwl.cwltoil.StepValueFrom method) do_GET() (toil.test.jobStores.jobStoreTest.StubHttpRequestHandler method) dockerCall() (in module toil.lib.docker) dockerCheckOutput() (in module toil.lib.docker) DockerCheckTest (class in toil.test.src.dockerCheckTest) dockerKill() (in module toil.lib.docker) (in module toil.test.lib.dockerTest) dockerName (in module toil.version) dockerRegistry (in module toil.common) (in module toil.version) dockerStop() (in module toil.lib.docker) dockerTag (in module toil.common) (in module toil.version) DockerTest (class in toil.test.lib.dockerTest) DomainDoesNotExist doubleMem (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) down() (in module toil.test.sort.restart_sort) (in module toil.test.sort.sort) download() (toil.batchSystems.abstractBatchSystem.Resource method) (toil.batchSystems.awsBatch.Resource method) (toil.batchSystems.contained_executor.Resource method) (toil.batchSystems.kubernetes.Resource method) (toil.batchSystems.mesos.executor.Resource method) (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo method) (toil.resource.Resource method) (toil.test.cwl.cwlTest.CWLWorkflowTest method) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo method) (toil.test.src.resourceTest.Resource method) download_directory() (toil.test.cwl.cwlTest.CWLWorkflowTest method) download_file_from_internet() (in module toil.server.utils) (in module toil.server.wes.tasks) download_file_from_s3() (in module toil.server.utils) (in module toil.server.wes.tasks) download_region_json() (in module toil.lib.ec2nodes) download_structure() (in module toil.cwl.cwltoil) (in module toil.cwl.utils) (in module toil.test.cwl.cwlTest) download_subdirectory() (toil.test.cwl.cwlTest.CWLWorkflowTest method) downloadStream() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo method) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo method) DownReturnType (in module toil.cwl.utils) drop_missing_files() (in module toil.wdl.wdltoil) duplicate_quotes() (toil.batchSystems.htcondor.HTCondorBatchSystem.GridEngineThread method)

E

E (in module toil.lib.retry) e() (in module toil.test.src.promisesTest) E2Instances (in module toil.lib.generatedEC2Lists) (in module toil.provisioners.aws.awsProvisioner) ec2InstancesByRegion (in module toil.lib.generatedEC2Lists) EC2Regions (in module toil.jobStores.aws.jobStore) (in module toil.lib.ec2nodes) emit() (toil.test.src.realtimeLoggerTest.MessageDetector method) empty() (toil.bus.MessageInbox method) enable_public_objects() (in module toil.jobStores.aws.jobStore) (in module toil.lib.aws.utils) enableUnlimitedPreemptibleRetries (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) encapsulate() (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.Job method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) EncapsulatedJob (class in toil.job) encapsulatedJobFn() (in module toil.test.src.jobEncapsulationTest) encode_directory() (in module toil.cwl.cwltoil) EncryptedAWSJobStoreTest (class in toil.test.jobStores.jobStoreTest) ensure_no_collisions() (in module toil.cwl.cwltoil) enter() (toil.batchSystems.cleanup_support.LastProcessStandingArena method) (toil.lib.threading.LastProcessStandingArena method) (toil.test.src.threadingTest.LastProcessStandingArena method) environment (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) EnvironmentTest (class in toil.test.src.environmentTest) envPrefix (toil.common.RealtimeLogger attribute) (toil.deferred.RealtimeLogger attribute) (toil.realtimeLogger.RealtimeLogger attribute) (toil.test.sort.restart_sort.RealtimeLogger attribute) (toil.test.sort.sort.RealtimeLogger attribute) (toil.test.src.fileStoreTest.RealtimeLogger attribute) (toil.test.src.realtimeLoggerTest.RealtimeLogger attribute) ERROR (toil.batchSystems.abstractBatchSystem.BatchJobExitReason attribute) (toil.batchSystems.abstractGridEngineBatchSystem.BatchJobExitReason attribute) (toil.batchSystems.awsBatch.BatchJobExitReason attribute) (toil.batchSystems.kubernetes.BatchJobExitReason attribute) (toil.batchSystems.lsf.BatchJobExitReason attribute) (toil.batchSystems.mesos.batchSystem.BatchJobExitReason attribute) (toil.batchSystems.slurm.BatchJobExitReason attribute) (toil.leader.BatchJobExitReason attribute) (toil.test.batchSystems.test_slurm.BatchJobExitReason attribute) (toil.test.src.busTest.BatchJobExitReason attribute) error() (toil.batchSystems.mesos.executor.MesosExecutor method) error_meets_conditions() (in module toil.lib.retry) errorChild() (in module toil.test.src.jobTest) ErrorCondition (class in toil.batchSystems.kubernetes) (class in toil.fileStores.cachingFileStore) (class in toil.fileStores.nonCachingFileStore) (class in toil.jobStores.abstractJobStore) (class in toil.lib.aws.utils) (class in toil.lib.ec2) (class in toil.lib.retry) (class in toil.provisioners.aws.awsProvisioner) (class in toil.resource) establish_boto3_session() (in module toil.batchSystems.awsBatch) (in module toil.jobStores.aws.jobStore) (in module toil.lib.aws.session) (in module toil.lib.ec2) (in module toil.test.lib.aws.test_s3) eval_prep() (toil.cwl.cwltoil.StepValueFrom method) evaluate_call_inputs() (in module toil.wdl.wdltoil) evaluate_decl() (in module toil.wdl.wdltoil) evaluate_defaultable_decl() (in module toil.wdl.wdltoil) evaluate_named_expression() (in module toil.wdl.wdltoil) evaluate_output_decls() (in module toil.wdl.wdltoil) evaluatePromisedRequirements() (toil.job.PromisedRequirementFunctionWrappingJob method) EVICTION_THRESHOLD (in module toil.provisioners.clusterScaler) ex_create_multiple_nodes() (toil.provisioners.gceProvisioner.GCEProvisioner method) exactPython (in module toil.resource) (in module toil.test.provisioners.aws.awsProvisionerTest) (in module toil.test.provisioners.gceProvisionerTest) (in module toil.test.src.autoDeploymentTest) (in module toil.test.src.resourceTest) (in module toil.test.wdl.wdltoil_test) (in module toil.version) exc_info (toil.batchSystems.mesos.test.ExceptionalThread attribute) (toil.cwl.cwltoil.ExceptionalThread attribute) (toil.jobStores.utils.ExceptionalThread attribute) (toil.lib.threading.ExceptionalThread attribute) (toil.provisioners.clusterScaler.ExceptionalThread attribute) (toil.test.ExceptionalThread attribute) ExceptionalThread (class in toil.batchSystems.mesos.test) (class in toil.cwl.cwltoil) (class in toil.jobStores.utils) (class in toil.lib.threading) (class in toil.provisioners.clusterScaler) (class in toil.test) executor() (in module toil.batchSystems.contained_executor) executorLost() (toil.batchSystems.mesos.batchSystem.MesosBatchSystem method) exists() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.ToilFsAccess method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo class method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.server.wes.toil_backend.ToilWorkflow method) (toil.serviceManager.AbstractJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo class method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method)

exit_code (toil.bus.JobCompletedMessage attribute) (toil.bus.JobStatus attribute) (toil.common.JobCompletedMessage attribute) (toil.leader.JobCompletedMessage attribute) (toil.server.wes.amazon_wes_utils.JobStatus attribute) (toil.server.wes.toil_backend.JobStatus attribute) (toil.test.src.busTest.JobCompletedMessage attribute) EXIT_STATUS_UNAVAILABLE_VALUE (in module toil.batchSystems.abstractBatchSystem) (in module toil.batchSystems.awsBatch) (in module toil.batchSystems.contained_executor) (in module toil.batchSystems.kubernetes) (in module toil.batchSystems.lsf) (in module toil.batchSystems.mesos.batchSystem) (in module toil.batchSystems.singleMachine) (in module toil.batchSystems.slurm) (in module toil.leader) (in module toil.test.batchSystems.test_slurm) exitReason (toil.batchSystems.abstractBatchSystem.UpdatedBatchJobInfo attribute) (toil.batchSystems.abstractGridEngineBatchSystem.UpdatedBatchJobInfo attribute) (toil.batchSystems.awsBatch.UpdatedBatchJobInfo attribute) (toil.batchSystems.kubernetes.UpdatedBatchJobInfo attribute) (toil.batchSystems.local_support.UpdatedBatchJobInfo attribute) (toil.batchSystems.mesos.batchSystem.UpdatedBatchJobInfo attribute) (toil.batchSystems.singleMachine.UpdatedBatchJobInfo attribute) (toil.batchSystems.torque.UpdatedBatchJobInfo attribute) (toil.test.batchSystems.batch_system_plugin_test.UpdatedBatchJobInfo attribute) exitStatus (toil.batchSystems.abstractBatchSystem.UpdatedBatchJobInfo attribute) (toil.batchSystems.abstractGridEngineBatchSystem.UpdatedBatchJobInfo attribute) (toil.batchSystems.awsBatch.UpdatedBatchJobInfo attribute) (toil.batchSystems.kubernetes.UpdatedBatchJobInfo attribute) (toil.batchSystems.local_support.UpdatedBatchJobInfo attribute) (toil.batchSystems.mesos.batchSystem.UpdatedBatchJobInfo attribute) (toil.batchSystems.singleMachine.UpdatedBatchJobInfo attribute) (toil.batchSystems.torque.UpdatedBatchJobInfo attribute) (toil.test.batchSystems.batch_system_plugin_test.UpdatedBatchJobInfo attribute) Expando (class in toil.batchSystems.mesos.executor) (class in toil.job) (class in toil.lib.expando) (class in toil.statsAndLogging) (class in toil.utils.toilStats) expectedShutdownErrors() (in module toil.provisioners.aws.awsProvisioner) export_file() (toil.batchSystems.abstractBatchSystem.AbstractFileStore method) (toil.batchSystems.abstractBatchSystem.Toil method) (toil.batchSystems.awsBatch.Toil method) (toil.batchSystems.cleanup_support.Toil method) (toil.batchSystems.kubernetes.Toil method) (toil.batchSystems.singleMachine.Toil method) (toil.common.Toil method) (toil.cwl.cwltoil.AbstractFileStore method) (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.Toil method) (toil.cwl.utils.AbstractFileStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractFileStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.abstractFileStore.Toil method) (toil.fileStores.cachingFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.CachingFileStore method) (toil.fileStores.nonCachingFileStore.AbstractFileStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.NonCachingFileStore method) (toil.job.Toil method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.server.wes.tasks.Toil method) (toil.serviceManager.AbstractJobStore method) (toil.test.batchSystems.batch_system_plugin_test.Toil method) (toil.test.batchSystems.batchSystemTest.Toil method) (toil.test.cwl.cwlTest.AbstractFileStore method) (toil.test.jobStores.jobStoreTest.Toil method) (toil.test.lib.dockerTest.Toil method) (toil.test.mesos.helloWorld.Toil method) (toil.test.options.options.Toil method) (toil.test.sort.restart_sort.Toil method) (toil.test.sort.sort.Toil method) (toil.test.sort.sortTest.Toil method) (toil.test.src.busTest.Toil method) (toil.test.src.environmentTest.Toil method) (toil.test.src.fileStoreTest.Toil method) (toil.test.src.importExportFileTest.Toil method) (toil.test.src.jobDescriptionTest.Toil method) (toil.test.src.jobFileStoreTest.Toil method) (toil.test.src.jobTest.Toil method) (toil.test.src.restartDAGTest.Toil method) (toil.test.src.toilContextManagerTest.Toil method) (toil.test.utils.toilKillTest.Toil method) (toil.test.utils.utilsTest.Toil method) (toil.toilState.AbstractJobStore method) (toil.utils.toilClean.Toil method) (toil.utils.toilDebugFile.Toil method) (toil.utils.toilDebugJob.Toil method) (toil.utils.toilKill.Toil method) (toil.utils.toilStats.AbstractJobStore method) (toil.utils.toilStats.Toil method) (toil.utils.toilStatus.Toil method) (toil.wdl.wdltoil.AbstractFileStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.wdl.wdltoil.Toil method) (toil.worker.AbstractFileStore method) (toil.worker.AbstractJobStore method) (toil.worker.Toil method) exportFile() (toil.batchSystems.abstractBatchSystem.AbstractFileStore method) (toil.batchSystems.abstractBatchSystem.Toil method) (toil.batchSystems.awsBatch.Toil method) (toil.batchSystems.cleanup_support.Toil method) (toil.batchSystems.kubernetes.Toil method) (toil.batchSystems.singleMachine.Toil method) (toil.common.Toil method) (toil.cwl.cwltoil.AbstractFileStore method) (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.Toil method) (toil.cwl.utils.AbstractFileStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractFileStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.abstractFileStore.Toil method) (toil.fileStores.cachingFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.CachingFileStore method) (toil.fileStores.nonCachingFileStore.AbstractFileStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.NonCachingFileStore method) (toil.job.Toil method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.server.wes.tasks.Toil method) (toil.serviceManager.AbstractJobStore method) (toil.test.batchSystems.batch_system_plugin_test.Toil method) (toil.test.batchSystems.batchSystemTest.Toil method) (toil.test.cwl.cwlTest.AbstractFileStore method) (toil.test.jobStores.jobStoreTest.Toil method) (toil.test.lib.dockerTest.Toil method) (toil.test.mesos.helloWorld.Toil method) (toil.test.options.options.Toil method) (toil.test.sort.restart_sort.Toil method) (toil.test.sort.sort.Toil method) (toil.test.sort.sortTest.Toil method) (toil.test.src.busTest.Toil method) (toil.test.src.environmentTest.Toil method) (toil.test.src.fileStoreTest.Toil method) (toil.test.src.importExportFileTest.Toil method) (toil.test.src.jobDescriptionTest.Toil method) (toil.test.src.jobFileStoreTest.Toil method) (toil.test.src.jobTest.Toil method) (toil.test.src.restartDAGTest.Toil method) (toil.test.src.toilContextManagerTest.Toil method) (toil.test.utils.toilKillTest.Toil method) (toil.test.utils.utilsTest.Toil method) (toil.toilState.AbstractJobStore method) (toil.utils.toilClean.Toil method) (toil.utils.toilDebugFile.Toil method) (toil.utils.toilDebugJob.Toil method) (toil.utils.toilKill.Toil method) (toil.utils.toilStats.AbstractJobStore method) (toil.utils.toilStats.Toil method) (toil.utils.toilStatus.Toil method) (toil.wdl.wdltoil.AbstractFileStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.wdl.wdltoil.Toil method) (toil.worker.AbstractFileStore method) (toil.worker.AbstractJobStore method) (toil.worker.Toil method) external_batch_id (toil.batchSystems.abstractGridEngineBatchSystem.ExternalBatchIdMessage attribute) (toil.batchSystems.awsBatch.ExternalBatchIdMessage attribute) (toil.batchSystems.singleMachine.ExternalBatchIdMessage attribute) (toil.bus.ExternalBatchIdMessage attribute) (toil.bus.JobStatus attribute) (toil.server.wes.amazon_wes_utils.JobStatus attribute) (toil.server.wes.toil_backend.JobStatus attribute) ExternalBatchIdMessage (class in toil.batchSystems.abstractGridEngineBatchSystem) (class in toil.batchSystems.awsBatch) (class in toil.batchSystems.singleMachine) (class in toil.bus) externalStoreCache (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test attribute) extract() (toil.cwl.cwltoil.CWLGather static method) extractFile() (toil.provisioners.abstractProvisioner.Node method) (toil.provisioners.aws.awsProvisioner.Node method) (toil.provisioners.gceProvisioner.Node method) (toil.provisioners.node.Node method) (toil.test.provisioners.clusterScalerTest.Node method)

F

F (in module toil.provisioners.aws.awsProvisioner) (in module toil.wdl.wdltoil) f0() (in module toil.test.provisioners.restartScript) FAILED (toil.batchSystems.abstractBatchSystem.BatchJobExitReason attribute) (toil.batchSystems.abstractGridEngineBatchSystem.BatchJobExitReason attribute) (toil.batchSystems.awsBatch.BatchJobExitReason attribute) (toil.batchSystems.kubernetes.BatchJobExitReason attribute) (toil.batchSystems.lsf.BatchJobExitReason attribute) (toil.batchSystems.mesos.batchSystem.BatchJobExitReason attribute) (toil.batchSystems.slurm.BatchJobExitReason attribute) (toil.leader.BatchJobExitReason attribute) (toil.test.batchSystems.test_slurm.BatchJobExitReason attribute) (toil.test.src.busTest.BatchJobExitReason attribute) FailedConstraint (in module toil.provisioners.clusterScaler) FailedJobsException, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] failing_job_fn() (in module toil.test.src.busTest) failingFn() (in module toil.test.src.restartDAGTest) FailOnce (class in toil.test.src.checkpointTest) FakeBatchSystem (class in toil.test.batchSystems.batch_system_plugin_test) (class in toil.test.batchSystems.test_slurm) fallbackGetJobExitCode() (toil.batchSystems.lsf.LSFBatchSystem.GridEngineThread method) fallbackRunningJobIDs() (toil.batchSystems.lsf.LSFBatchSystem.GridEngineThread method) fC() (in module toil.options.common) feed_deadlock_watchdog() (toil.leader.Leader method) feed_flatcar_ami_release() (in module toil.lib.aws.ami) (in module toil.test.lib.test_ec2) fetch_scratch() (toil.server.wes.toil_backend.ToilWorkflow method) fetch_state() (toil.server.wes.toil_backend.ToilWorkflow method) fetch_url() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) fetchFiles() (in module toil.test.utils.toilDebugTest) fetchJobStoreFiles() (in module toil.utils.toilDebugFile) fetchRootJob() (toil.test.utils.utilsTest.ToilStatus method) (toil.utils.toilDebugJob.ToilStatus method) (toil.utils.toilStatus.ToilStatus method) fetchUserJobs() (toil.test.utils.utilsTest.ToilStatus method) (toil.utils.toilDebugJob.ToilStatus method) (toil.utils.toilStatus.ToilStatus method) file_exists() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) file_store_id (toil.job.JobBodyReference attribute) fileContents (toil.test.jobStores.jobStoreTest.StubHttpRequestHandler attribute) fileExists() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) FileID (class in toil.common) (class in toil.cwl.cwltoil) (class in toil.cwl.utils) (class in toil.fileStores) (class in toil.fileStores.abstractFileStore) (class in toil.fileStores.cachingFileStore) (class in toil.fileStores.nonCachingFileStore) (class in toil.job) (class in toil.jobStores.abstractJobStore) (class in toil.jobStores.aws.jobStore) (class in toil.jobStores.fileJobStore) (class in toil.test.cwl.cwlTest) (class in toil.test.jobStores.jobStoreTest) (class in toil.test.src.fileStoreTest) (class in toil.test.src.importExportFileTest) (class in toil.test.src.jobFileStoreTest) (class in toil.wdl.wdltoil) fileID (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo property) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo property) fileIsCached() (toil.fileStores.cachingFileStore.CachingFileStore method) FileJobStore (class in toil.cwl.cwltoil) (class in toil.jobStores.fileJobStore) (class in toil.test.jobStores.jobStoreTest) (class in toil.test.src.workerTest) (class in toil.utils.toilDebugFile) (class in toil.utils.toilDebugJob) FileJobStoreTest (class in toil.test.jobStores.jobStoreTest) FileResource (class in toil.resource) files (toil.server.wes.amazon_wes_utils.WorkflowPlan attribute) files_downloaded_hook() (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.Job method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) FilesDict (class in toil.server.wes.amazon_wes_utils) FilesDownloadedStoppingPointReached, [1] fileSizeAndTime() (in module toil.jobStores.aws.jobStore) (in module toil.jobStores.aws.utils) FileStateStore (class in toil.server.utils) FileStateStoreTest (class in toil.test.server.serverTest) FileStateStoreURLTest (class in toil.test.server.serverTest) filesToDelete (toil.cwl.cwltoil.Promise attribute) (toil.job.Promise attribute) (toil.wdl.wdltoil.Promise attribute) fileStore (toil.job.JobFunctionWrappingJob property) (toil.job.ServiceHostJob property) (toil.test.src.jobTest.JobFunctionWrappingJob property) fileStoreChild() (in module toil.test.src.jobFileStoreTest) fileStoreString (in module toil.test.src.jobFileStoreTest) fileTestJob() (in module toil.test.src.jobFileStoreTest) filter_out_static_nodes() (toil.provisioners.clusterScaler.ClusterScaler method) (toil.test.provisioners.clusterScalerTest.ClusterScaler method) filter_skip_null() (in module toil.cwl.cwltoil) filtered_secondary_files() (in module toil.cwl.cwltoil)

filterServiceHosts() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) filterSuccessors() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) find() (in module toil.batchSystems.lsfHelper) find_default_container() (in module toil.cwl.cwltoil) find_first_match() (in module toil.batchSystems.lsfHelper) findMesosBinary() (toil.batchSystems.mesos.test.MesosTestSupport.MesosThread method) (toil.test.batchSystems.batchSystemTest.MesosTestSupport.MesosThread method) (toil.test.sort.sortTest.MesosTestSupport.MesosThread method) (toil.test.src.promisedRequirementTest.MesosTestSupport.MesosThread method) FINISHED (toil.batchSystems.abstractBatchSystem.BatchJobExitReason attribute) (toil.batchSystems.abstractGridEngineBatchSystem.BatchJobExitReason attribute) (toil.batchSystems.awsBatch.BatchJobExitReason attribute) (toil.batchSystems.kubernetes.BatchJobExitReason attribute) (toil.batchSystems.lsf.BatchJobExitReason attribute) (toil.batchSystems.mesos.batchSystem.BatchJobExitReason attribute) (toil.batchSystems.slurm.BatchJobExitReason attribute) (toil.leader.BatchJobExitReason attribute) (toil.test.batchSystems.test_slurm.BatchJobExitReason attribute) (toil.test.src.busTest.BatchJobExitReason attribute) fits() (toil.provisioners.clusterScaler.NodeReservation method) (toil.test.provisioners.clusterScalerTest.NodeReservation method) flat_crossproduct_scatter() (toil.cwl.cwltoil.CWLScatter method) flatcar_release_feed_amis() (in module toil.lib.aws.ami) (in module toil.test.lib.test_ec2) FlatcarFeedTest (class in toil.test.lib.test_ec2) flatten() (in module toil.lib.iterables) flatten_tags() (in module toil.jobStores.aws.jobStore) (in module toil.lib.aws.utils) (in module toil.lib.ec2) (in module toil.provisioners.aws.awsProvisioner) flush() (toil.fileStores.abstractFileStore.WriteWatchingStream method) (toil.jobStores.abstractJobStore.WriteWatchingStream method) (toil.lib.io.WriteWatchingStream method) fn1Test() (in module toil.test.src.jobEncapsulationTest) (in module toil.test.src.jobTest) fn2Test() (in module toil.test.src.jobTest) fnTest() (in module toil.test.src.jobServiceTest) FollowOn (class in toil.test.src.helloWorldTest) (class in toil.test.src.toilContextManagerTest) Foo (class in toil.test.src.userDefinedJobArgTypeTest) for_each() (toil.bus.MessageInbox method) for_each_node() (in module toil.wdl.wdltoil) forceDockerAppliance (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) forgetJob() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.slurm.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.torque.AbstractGridEngineBatchSystem.GridEngineThread method) FORGO (in module toil.lib.docker) (in module toil.test.lib.dockerTest) format_std_out_err_glob() (toil.batchSystems.abstractBatchSystem.BatchSystemSupport method) (toil.batchSystems.cleanup_support.BatchSystemSupport method) (toil.batchSystems.local_support.BatchSystemSupport method) (toil.batchSystems.mesos.executor.BatchSystemSupport method) (toil.batchSystems.singleMachine.BatchSystemSupport method) (toil.test.batchSystems.batchSystemTest.BatchSystemSupport method) format_std_out_err_path() (toil.batchSystems.abstractBatchSystem.BatchSystemSupport method) (toil.batchSystems.cleanup_support.BatchSystemSupport method) (toil.batchSystems.local_support.BatchSystemSupport method) (toil.batchSystems.mesos.executor.BatchSystemSupport method) (toil.batchSystems.singleMachine.BatchSystemSupport method) (toil.test.batchSystems.batchSystemTest.BatchSystemSupport method) formatLogStream() (toil.exceptions.StatsAndLogging class method) (toil.leader.StatsAndLogging class method) (toil.statsAndLogging.StatsAndLogging class method) (toil.test.jobStores.jobStoreTest.StatsAndLogging class method) (toil.utils.toilStatus.StatsAndLogging class method) forModule() (toil.deferred.ModuleDescriptor class method) (toil.job.ModuleDescriptor class method) (toil.resource.ModuleDescriptor class method) (toil.test.src.jobDescriptionTest.ModuleDescriptor class method) (toil.test.src.resourceTest.ModuleDescriptor class method) forPath() (toil.common.FileID class method) (toil.cwl.cwltoil.FileID class method) (toil.cwl.utils.FileID class method) (toil.fileStores.abstractFileStore.FileID class method) (toil.fileStores.cachingFileStore.FileID class method) (toil.fileStores.FileID class method) (toil.fileStores.nonCachingFileStore.FileID class method) (toil.job.FileID class method) (toil.jobStores.abstractJobStore.FileID class method) (toil.jobStores.aws.jobStore.FileID class method) (toil.jobStores.fileJobStore.FileID class method) (toil.test.cwl.cwlTest.FileID class method) (toil.test.jobStores.jobStoreTest.FileID class method) (toil.test.src.fileStoreTest.FileID class method) (toil.test.src.importExportFileTest.FileID class method) (toil.test.src.jobFileStoreTest.FileID class method) (toil.wdl.wdltoil.FileID class method) frameworkMessage() (toil.batchSystems.mesos.batchSystem.MesosBatchSystem method) (toil.batchSystems.mesos.executor.MesosExecutor method) fromCommand() (toil.deferred.ModuleDescriptor class method) (toil.job.ModuleDescriptor class method) (toil.resource.ModuleDescriptor class method) (toil.test.src.jobDescriptionTest.ModuleDescriptor class method) (toil.test.src.resourceTest.ModuleDescriptor class method) fromItem() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo class method) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo class method) full_policy() (toil.provisioners.aws.awsProvisioner.AWSProvisioner method) (toil.test.provisioners.aws.awsProvisionerTest.AWSProvisioner method) FunctionWrappingJob (class in toil.job)

G

GCEAutoscaleTest (class in toil.test.provisioners.gceProvisionerTest) GCEAutoscaleTestMultipleNodeTypes (class in toil.test.provisioners.gceProvisionerTest) GCEProvisioner (class in toil.provisioners.gceProvisioner) GCERestartTest (class in toil.test.provisioners.gceProvisionerTest) GCEStaticAutoscaleTest (class in toil.test.provisioners.gceProvisionerTest) gen_message_bus_path() (in module toil.bus) (in module toil.leader) generate_attachment_path_names() (in module toil.server.cli.wes_cwl_runner) generate_config() (in module toil.common) (in module toil.utils.toilConfig) generate_default_job_store() (in module toil.cwl.cwltoil) generate_locator() (in module toil.cwl.cwltoil) (in module toil.jobStores.utils) (in module toil.server.wes.tasks) (in module toil.test.utils.toilKillTest) generateTorqueWrapper() (toil.batchSystems.torque.TorqueBatchSystem.GridEngineThread method) get() (in module toil.utils.toilStats) (toil.server.utils.AbstractStateStore method) (toil.server.utils.FileStateStore method) (toil.server.utils.MemoryStateCache method) (toil.server.utils.S3StateStore method) (toil.server.utils.WorkflowStateStore method) (toil.test.wdl.wdltoil_test.WDLWorkflowGraph method) (toil.wdl.wdltoil.WDLWorkflowGraph method) get_actions_from_policy_document() (in module toil.lib.aws.iam) get_attributes_from_item() (toil.jobStores.aws.jobStore.SDBHelper class method) (toil.jobStores.aws.utils.SDBHelper class method) get_aws_account_num() (in module toil.lib.aws.iam) get_aws_zone_from_boto() (in module toil.lib.aws) (in module toil.provisioners.aws) get_aws_zone_from_environment() (in module toil.lib.aws) (in module toil.provisioners.aws) get_aws_zone_from_environment_region() (in module toil.lib.aws) (in module toil.provisioners.aws) get_aws_zone_from_metadata() (in module toil.lib.aws) (in module toil.provisioners.aws) get_aws_zone_from_spot_market() (in module toil.provisioners.aws) get_batch_logs_dir() (toil.batchSystems.abstractBatchSystem.BatchSystemSupport method) (toil.batchSystems.cleanup_support.BatchSystemSupport method) (toil.batchSystems.local_support.BatchSystemSupport method) (toil.batchSystems.mesos.executor.BatchSystemSupport method) (toil.batchSystems.singleMachine.BatchSystemSupport method) (toil.test.batchSystems.batchSystemTest.BatchSystemSupport method) get_batch_system() (in module toil.batchSystems.options) (in module toil.batchSystems.registry) (in module toil.test.batchSystems.batchSystemTest) get_batch_systems() (in module toil.batchSystems.options) (in module toil.batchSystems.registry) (in module toil.test.batchSystems.batchSystemTest) get_best_aws_zone() (in module toil.provisioners.aws) (in module toil.provisioners.aws.awsProvisioner) (in module toil.test.provisioners.clusterTest) get_body() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) get_bucket_region() (in module toil.jobStores.aws.jobStore) (in module toil.jobStores.aws.utils) (in module toil.lib.aws.utils) (in module toil.test.lib.aws.test_s3) get_chain() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) get_client() (in module toil.lib.aws.iam) (in module toil.provisioners.aws.awsProvisioner) get_conf_file() (in module toil.batchSystems.lsfHelper) get_container_engine() (in module toil.cwl.cwltoil) get_current_aws_region() (in module toil.batchSystems.awsBatch) (in module toil.lib.aws) (in module toil.server.app) get_current_aws_zone() (in module toil.lib.aws) get_current_state() (toil.server.utils.WorkflowStateMachine method) (toil.server.wes.tasks.WorkflowStateMachine method) (toil.server.wes.toil_backend.WorkflowStateMachine method) get_default_kubernetes_owner() (toil.batchSystems.kubernetes.KubernetesBatchSystem class method) get_default_mesos_endpoint() (toil.batchSystems.mesos.batchSystem.MesosBatchSystem class method) get_dependencies() (toil.test.wdl.wdltoil_test.WDLWorkflowGraph method) (toil.wdl.wdltoil.WDLWorkflowGraph method) get_deps_from_cwltool() (in module toil.server.cli.wes_cwl_runner) get_disk_usage() (toil.batchSystems.abstractBatchSystem.AbstractFileStore method) (toil.cwl.cwltoil.AbstractFileStore method) (toil.cwl.utils.AbstractFileStore method) (toil.fileStores.abstractFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.AbstractFileStore method) (toil.fileStores.nonCachingFileStore.AbstractFileStore method) (toil.test.cwl.cwlTest.AbstractFileStore method) (toil.wdl.wdltoil.AbstractFileStore method) (toil.worker.AbstractFileStore method) get_empty_file_store_id() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) get_env() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) get_error_body() (in module toil.lib.retry) (in module toil.provisioners.aws.awsProvisioner) get_error_code() (in module toil.jobStores.aws.jobStore) (in module toil.jobStores.aws.utils) (in module toil.lib.aws.utils) (in module toil.lib.ec2) (in module toil.lib.retry) (in module toil.provisioners.aws.awsProvisioner) get_error_message() (in module toil.jobStores.aws.utils) (in module toil.lib.ec2) (in module toil.lib.retry) (in module toil.provisioners.aws.awsProvisioner) get_error_status() (in module toil.jobStores.aws.jobStore) (in module toil.jobStores.aws.utils) (in module toil.lib.aws.utils) (in module toil.lib.retry) (in module toil.provisioners.aws.awsProvisioner) get_failed_constraints() (toil.provisioners.clusterScaler.NodeReservation method) (toil.test.provisioners.clusterScalerTest.NodeReservation method) get_file_class() (in module toil.server.utils) (in module toil.server.wes.tasks) get_file_paths_in_bindings() (in module toil.wdl.wdltoil) get_file_size() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) get_flatcar_ami() (in module toil.lib.aws.ami) (in module toil.provisioners.aws.awsProvisioner) (in module toil.test.lib.test_ec2) get_free_snapshot() (toil.batchSystems.abstractBatchSystem.ResourceSet method) (toil.batchSystems.singleMachine.ResourceSet method) get_from_structure() (in module toil.cwl.cwltoil) (in module toil.cwl.utils) get_health() (toil.server.app.ToilBackend method) (toil.server.wes.toil_backend.ToilBackend method) get_homepage() (toil.server.app.ToilBackend method) (toil.server.wes.toil_backend.ToilBackend method) get_host_accelerator_numbers() (in module toil.lib.accelerators) (in module toil.lib.docker) get_individual_local_accelerators() (in module toil.batchSystems.singleMachine) (in module toil.lib.accelerators) get_is_directory() (toil.cwl.cwltoil.AbstractJobStore class method) (toil.cwl.utils.AbstractJobStore class method) (toil.fileStores.abstractFileStore.AbstractJobStore class method) (toil.fileStores.cachingFileStore.AbstractJobStore class method) (toil.fileStores.nonCachingFileStore.AbstractJobStore class method) (toil.jobStores.abstractJobStore.AbstractJobStore class method) (toil.jobStores.aws.jobStore.AbstractJobStore class method) (toil.jobStores.fileJobStore.AbstractJobStore class method) (toil.jobStores.googleJobStore.AbstractJobStore class method) (toil.leader.AbstractJobStore class method) (toil.serviceManager.AbstractJobStore class method) (toil.toilState.AbstractJobStore class method) (toil.utils.toilStats.AbstractJobStore class method) (toil.wdl.wdltoil.AbstractJobStore class method) (toil.worker.AbstractJobStore class method) get_iso_time() (in module toil.server.utils) (in module toil.server.wes.tasks) get_item_from_attributes() (in module toil.jobStores.aws.jobStore) (in module toil.lib.aws.utils) get_job() (toil.leader.ToilState method) (toil.serviceManager.ToilState method) (toil.toilState.ToilState method) get_job_count() (toil.leader.ServiceManager method) (toil.serviceManager.ServiceManager method) get_job_kind() (in module toil.batchSystems.abstractGridEngineBatchSystem) (in module toil.bus) (in module toil.leader) get_local_workflow_coordination_dir() (toil.batchSystems.abstractBatchSystem.Toil class method) (toil.batchSystems.awsBatch.Toil class method) (toil.batchSystems.cleanup_support.Toil class method) (toil.batchSystems.kubernetes.Toil class method) (toil.batchSystems.singleMachine.Toil class method) (toil.common.Toil class method) (toil.cwl.cwltoil.Toil class method) (toil.fileStores.abstractFileStore.Toil class method) (toil.job.Toil class method) (toil.server.wes.tasks.Toil class method) (toil.test.batchSystems.batch_system_plugin_test.Toil class method) (toil.test.batchSystems.batchSystemTest.Toil class method) (toil.test.jobStores.jobStoreTest.Toil class method) (toil.test.lib.dockerTest.Toil class method) (toil.test.mesos.helloWorld.Toil class method) (toil.test.options.options.Toil class method) (toil.test.sort.restart_sort.Toil class method) (toil.test.sort.sort.Toil class method) (toil.test.sort.sortTest.Toil class method) (toil.test.src.busTest.Toil class method) (toil.test.src.environmentTest.Toil class method) (toil.test.src.fileStoreTest.Toil class method) (toil.test.src.importExportFileTest.Toil class method) (toil.test.src.jobDescriptionTest.Toil class method) (toil.test.src.jobFileStoreTest.Toil class method) (toil.test.src.jobTest.Toil class method) (toil.test.src.restartDAGTest.Toil class method) (toil.test.src.toilContextManagerTest.Toil class method) (toil.test.utils.toilKillTest.Toil class method) (toil.test.utils.utilsTest.Toil class method) (toil.utils.toilClean.Toil class method) (toil.utils.toilDebugFile.Toil class method) (toil.utils.toilDebugJob.Toil class method) (toil.utils.toilKill.Toil class method) (toil.utils.toilStats.Toil class method) (toil.utils.toilStatus.Toil class method) (toil.wdl.wdltoil.Toil class method) (toil.worker.Toil class method) get_lsf_units() (in module toil.batchSystems.lsfHelper) get_lsf_units_from_stream() (in module toil.batchSystems.lsfHelper) get_lsf_version() (in module toil.batchSystems.lsfHelper) get_max_startup_seconds() (toil.test.batchSystems.batchSystemTest.AWSBatchBatchSystemTest method) (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemTest method) get_messages_path() (toil.server.wes.toil_backend.ToilWorkflow method) get_names() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) get_object_for_url() (in module toil.jobStores.aws.jobStore) (in module toil.lib.aws.utils) get_omp_threads() (in module toil.test.batchSystems.batchSystemTest) get_options() (in module toil.cwl.cwltoil) get_or_die() (in module toil.utils.toilMain) get_output_files() (toil.server.wes.toil_backend.ToilWorkflow method) get_policy_permissions() (in module toil.lib.aws.iam) (in module toil.provisioners.aws.awsProvisioner) get_process_name() (in module toil.fileStores.cachingFileStore) (in module toil.fileStores.nonCachingFileStore) (in module toil.lib.threading) get_public_ip() (in module toil.batchSystems.mesos.batchSystem) (in module toil.lib.misc) (in module toil.realtimeLogger) get_public_url() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) get_ready_client() (toil.leader.ServiceManager method) (toil.serviceManager.ServiceManager method) get_restrictive_environment_for_local_accelerators() (in module toil.batchSystems.singleMachine) (in module toil.lib.accelerators) get_root_job_return_value() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) get_run_log() (toil.server.app.ToilBackend method) (toil.server.wes.abstract_backend.WESBackend method) (toil.server.wes.toil_backend.ToilBackend method) (toil.server.wes.toil_backend.WESBackend method) get_run_status() (toil.server.app.ToilBackend method) (toil.server.wes.abstract_backend.WESBackend method) (toil.server.wes.toil_backend.ToilBackend method) (toil.server.wes.toil_backend.WESBackend method) get_runs() (toil.server.app.ToilBackend method) (toil.server.wes.toil_backend.ToilBackend method) get_service_info() (toil.server.app.ToilBackend method) (toil.server.wes.abstract_backend.WESBackend method) (toil.server.wes.toil_backend.ToilBackend method) (toil.server.wes.toil_backend.WESBackend method) get_shared_public_url() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) get_size() (toil.cwl.cwltoil.AbstractJobStore class method) (toil.cwl.utils.AbstractJobStore class method) (toil.fileStores.abstractFileStore.AbstractJobStore class method) (toil.fileStores.cachingFileStore.AbstractJobStore class method) (toil.fileStores.nonCachingFileStore.AbstractJobStore class method) (toil.jobStores.abstractJobStore.AbstractJobStore class method) (toil.jobStores.aws.jobStore.AbstractJobStore class method) (toil.jobStores.fileJobStore.AbstractJobStore class method) (toil.jobStores.googleJobStore.AbstractJobStore class method) (toil.leader.AbstractJobStore class method) (toil.serviceManager.AbstractJobStore class method) (toil.toilState.AbstractJobStore class method) (toil.utils.toilStats.AbstractJobStore class method) (toil.wdl.wdltoil.AbstractJobStore class method) (toil.worker.AbstractJobStore class method) get_startable_service() (toil.leader.ServiceManager method) (toil.serviceManager.ServiceManager method) get_state() (toil.server.app.ToilBackend method) (toil.server.wes.tasks.ToilWorkflowRunner method) (toil.server.wes.toil_backend.ToilBackend method) (toil.server.wes.toil_backend.ToilWorkflow method) get_state_store() (toil.test.server.serverTest.AWSStateStoreTest method) (toil.test.server.serverTest.FileStateStoreTest method) (toil.test.server.serverTest.FileStateStoreURLTest method) (toil.test.server.serverTest.hidden.AbstractStateStoreTest method) get_stats() (in module toil.test.utils.utilsTest) (in module toil.utils.toilStats) get_stderr() (toil.server.app.ToilBackend method) (toil.server.wes.toil_backend.ToilBackend method) get_stderr_path() (toil.server.wes.toil_backend.ToilWorkflow method) get_stdout() (toil.server.app.ToilBackend method) (toil.server.wes.toil_backend.ToilBackend method) get_stdout_path() (toil.server.wes.toil_backend.ToilWorkflow method) get_supertype() (in module toil.wdl.wdltoil) get_task_logs() (toil.server.wes.toil_backend.ToilWorkflow method) get_temp_file() (in module toil.lib.bioio) (in module toil.test) (in module toil.test.src.busTest) (in module toil.test.src.jobEncapsulationTest) (in module toil.test.src.jobServiceTest) (in module toil.test.src.jobTest) (in module toil.test.src.toilContextManagerTest) (in module toil.test.utils.utilsTest) get_toil_coordination_dir() (toil.batchSystems.abstractBatchSystem.Toil class method) (toil.batchSystems.awsBatch.Toil class method) (toil.batchSystems.cleanup_support.Toil class method) (toil.batchSystems.kubernetes.Toil class method) (toil.batchSystems.singleMachine.Toil class method) (toil.common.Toil class method) (toil.cwl.cwltoil.Toil class method) (toil.fileStores.abstractFileStore.Toil class method) (toil.job.Toil class method) (toil.server.wes.tasks.Toil class method) (toil.test.batchSystems.batch_system_plugin_test.Toil class method) (toil.test.batchSystems.batchSystemTest.Toil class method) (toil.test.jobStores.jobStoreTest.Toil class method) (toil.test.lib.dockerTest.Toil class method) (toil.test.mesos.helloWorld.Toil class method) (toil.test.options.options.Toil class method) (toil.test.sort.restart_sort.Toil class method) (toil.test.sort.sort.Toil class method) (toil.test.sort.sortTest.Toil class method) (toil.test.src.busTest.Toil class method) (toil.test.src.environmentTest.Toil class method) (toil.test.src.fileStoreTest.Toil class method) (toil.test.src.importExportFileTest.Toil class method) (toil.test.src.jobDescriptionTest.Toil class method) (toil.test.src.jobFileStoreTest.Toil class method) (toil.test.src.jobTest.Toil class method) (toil.test.src.restartDAGTest.Toil class method) (toil.test.src.toilContextManagerTest.Toil class method) (toil.test.utils.toilKillTest.Toil class method) (toil.test.utils.utilsTest.Toil class method) (toil.utils.toilClean.Toil class method) (toil.utils.toilDebugFile.Toil class method) (toil.utils.toilDebugJob.Toil class method) (toil.utils.toilKill.Toil class method) (toil.utils.toilStats.Toil class method) (toil.utils.toilStatus.Toil class method) (toil.wdl.wdltoil.Toil class method) (toil.worker.Toil class method) get_total_cpu_time() (toil.job.ResourceMonitor class method) (toil.lib.resources.ResourceMonitor class method) (toil.statsAndLogging.ResourceMonitor class method) (toil.wdl.wdltoil.ResourceMonitor class method) (toil.worker.ResourceMonitor class method) get_total_cpu_time_and_memory_usage() (toil.job.ResourceMonitor class method) (toil.lib.resources.ResourceMonitor class method) (toil.statsAndLogging.ResourceMonitor class method) (toil.wdl.wdltoil.ResourceMonitor class method) (toil.worker.ResourceMonitor class method) get_transitive_dependencies() (toil.test.wdl.wdltoil_test.WDLWorkflowGraph method) (toil.wdl.wdltoil.WDLWorkflowGraph method) get_unservable_client() (toil.leader.ServiceManager method) (toil.serviceManager.ServiceManager method) get_user_name() (in module toil.batchSystems.kubernetes) (in module toil.batchSystems.mesos.batchSystem) (in module toil.lib.misc) (in module toil.test.lib.test_misc) (in module toil.wdl.wdltoil) get_version() (in module toil.wdl.utils) (toil.server.cli.wes_cwl_runner.WESClientWithWorkflowEngineParameters method) get_wdl_version() (in module toil.server.cli.wes_cwl_runner) get_width() (toil.utils.toilStats.ColumnWidths method) get_workflow_path_component() (toil.batchSystems.abstractBatchSystem.Toil static method) (toil.batchSystems.awsBatch.Toil static method) (toil.batchSystems.cleanup_support.Toil static method) (toil.batchSystems.kubernetes.Toil static method) (toil.batchSystems.singleMachine.Toil static method) (toil.common.Toil static method) (toil.cwl.cwltoil.Toil static method) (toil.fileStores.abstractFileStore.Toil static method) (toil.job.Toil static method) (toil.server.wes.tasks.Toil static method) (toil.test.batchSystems.batch_system_plugin_test.Toil static method) (toil.test.batchSystems.batchSystemTest.Toil static method) (toil.test.jobStores.jobStoreTest.Toil static method) (toil.test.lib.dockerTest.Toil static method) (toil.test.mesos.helloWorld.Toil static method) (toil.test.options.options.Toil static method) (toil.test.sort.restart_sort.Toil static method) (toil.test.sort.sort.Toil static method) (toil.test.sort.sortTest.Toil static method) (toil.test.src.busTest.Toil static method) (toil.test.src.environmentTest.Toil static method) (toil.test.src.fileStoreTest.Toil static method) (toil.test.src.importExportFileTest.Toil static method) (toil.test.src.jobDescriptionTest.Toil static method) (toil.test.src.jobFileStoreTest.Toil static method) (toil.test.src.jobTest.Toil static method) (toil.test.src.restartDAGTest.Toil static method) (toil.test.src.toilContextManagerTest.Toil static method) (toil.test.utils.toilKillTest.Toil static method) (toil.test.utils.utilsTest.Toil static method) (toil.utils.toilClean.Toil static method) (toil.utils.toilDebugFile.Toil static method) (toil.utils.toilDebugJob.Toil static method) (toil.utils.toilKill.Toil static method) (toil.utils.toilStats.Toil static method) (toil.utils.toilStatus.Toil static method) (toil.wdl.wdltoil.Toil static method) (toil.worker.Toil static method) getAdjacencyList() (toil.test.src.jobTest.JobTest static method) getAutoscaledInstanceShapes() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) getAverageRuntime() (toil.provisioners.clusterScaler.ClusterScaler method) (toil.test.provisioners.clusterScalerTest.ClusterScaler method) getBaseInstanceConfiguration() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) getBatchSystemID() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.slurm.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.torque.AbstractGridEngineBatchSystem.GridEngineThread method) getBatchSystemName() (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemJobTest method) (toil.test.batchSystems.batchSystemTest.MesosBatchSystemJobTest method) (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystemJobTest method) (toil.test.src.promisedRequirementTest.MesosPromisedRequirementsTest method) (toil.test.src.promisedRequirementTest.SingleMachinePromisedRequirementsTest method) getCacheAvailable() (toil.fileStores.cachingFileStore.CachingFileStore method) getCacheExtraJobSpace() (toil.fileStores.cachingFileStore.CachingFileStore method) getCacheLimit() (toil.fileStores.cachingFileStore.CachingFileStore method) getCacheUnusedJobRequirement() (toil.fileStores.cachingFileStore.CachingFileStore method) getCacheUsed() (toil.fileStores.cachingFileStore.CachingFileStore method) getContainerName() (in module toil.lib.docker) getCounterPath() (toil.test.src.promisedRequirementTest.hidden.AbstractPromisedRequirementsTest method) getCounters() (in module toil.test.batchSystems.batchSystemTest) getDefaultArgumentParser() (toil.cwl.cwltoil.Job.Runner static method) (toil.fileStores.abstractFileStore.Job.Runner static method) (toil.fileStores.cachingFileStore.Job.Runner static method) (toil.fileStores.nonCachingFileStore.Job.Runner static method) (toil.job.Job.Runner static method) (toil.jobStores.aws.jobStore.Job.Runner static method) (toil.test.batchSystems.batchSystemTest.Job.Runner static method) (toil.test.jobStores.jobStoreTest.Job.Runner static method) (toil.test.lib.dockerTest.Job.Runner static method) (toil.test.mesos.helloWorld.Job.Runner static method) (toil.test.mesos.stress.Job.Runner static method) (toil.test.provisioners.restartScript.Job.Runner static method) (toil.test.sort.restart_sort.Job.Runner static method) (toil.test.sort.sort.Job.Runner static method) (toil.test.sort.sortTest.Job.Runner static method) (toil.test.src.busTest.Job.Runner static method) (toil.test.src.checkpointTest.Job.Runner static method) (toil.test.src.deferredFunctionTest.Job.Runner static method) (toil.test.src.environmentTest.Job.Runner static method) (toil.test.src.fileStoreTest.Job.Runner static method) (toil.test.src.helloWorldTest.Job.Runner static method) (toil.test.src.importExportFileTest.Job.Runner static method) (toil.test.src.jobDescriptionTest.Job.Runner static method) (toil.test.src.jobEncapsulationTest.Job.Runner static method) (toil.test.src.jobFileStoreTest.Job.Runner static method) (toil.test.src.jobServiceTest.Job.Runner static method) (toil.test.src.jobTest.Job.Runner static method) (toil.test.src.promisedRequirementTest.Job.Runner static method) (toil.test.src.promisesTest.Job.Runner static method) (toil.test.src.realtimeLoggerTest.Job.Runner static method) (toil.test.src.restartDAGTest.Job.Runner static method) (toil.test.src.resumabilityTest.Job.Runner static method) (toil.test.src.retainTempDirTest.Job.Runner static method) (toil.test.src.toilContextManagerTest.Job.Runner static method) (toil.test.src.userDefinedJobArgTypeTest.Job.Runner static method) (toil.test.utils.utilsTest.Job.Runner static method) (toil.utils.toilStats.Job.Runner static method) (toil.wdl.wdltoil.Job.Runner static method) (toil.worker.Job.Runner static method) getDefaultOptions() (toil.cwl.cwltoil.Job.Runner static method) (toil.fileStores.abstractFileStore.Job.Runner static method) (toil.fileStores.cachingFileStore.Job.Runner static method) (toil.fileStores.nonCachingFileStore.Job.Runner static method) (toil.job.Job.Runner static method) (toil.jobStores.aws.jobStore.Job.Runner static method) (toil.test.batchSystems.batchSystemTest.Job.Runner static method) (toil.test.jobStores.jobStoreTest.Job.Runner static method) (toil.test.lib.dockerTest.Job.Runner static method) (toil.test.mesos.helloWorld.Job.Runner static method) (toil.test.mesos.stress.Job.Runner static method) (toil.test.provisioners.restartScript.Job.Runner static method) (toil.test.sort.restart_sort.Job.Runner static method) (toil.test.sort.sort.Job.Runner static method) (toil.test.sort.sortTest.Job.Runner static method) (toil.test.src.busTest.Job.Runner static method) (toil.test.src.checkpointTest.Job.Runner static method) (toil.test.src.deferredFunctionTest.Job.Runner static method) (toil.test.src.environmentTest.Job.Runner static method) (toil.test.src.fileStoreTest.Job.Runner static method) (toil.test.src.helloWorldTest.Job.Runner static method) (toil.test.src.importExportFileTest.Job.Runner static method) (toil.test.src.jobDescriptionTest.Job.Runner static method) (toil.test.src.jobEncapsulationTest.Job.Runner static method) (toil.test.src.jobFileStoreTest.Job.Runner static method) (toil.test.src.jobServiceTest.Job.Runner static method) (toil.test.src.jobTest.Job.Runner static method) (toil.test.src.promisedRequirementTest.Job.Runner static method) (toil.test.src.promisesTest.Job.Runner static method) (toil.test.src.realtimeLoggerTest.Job.Runner static method) (toil.test.src.restartDAGTest.Job.Runner static method) (toil.test.src.resumabilityTest.Job.Runner static method) (toil.test.src.retainTempDirTest.Job.Runner static method) (toil.test.src.toilContextManagerTest.Job.Runner static method) (toil.test.src.userDefinedJobArgTypeTest.Job.Runner static method) (toil.test.utils.utilsTest.Job.Runner static method) (toil.utils.toilStats.Job.Runner static method) (toil.wdl.wdltoil.Job.Runner static method) (toil.worker.Job.Runner static method)

getDirSizeRecursively() (in module toil.common) (in module toil.fileStores.abstractFileStore) getEmptyFileStoreID() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) getEnv() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) getEnvString() (toil.batchSystems.htcondor.HTCondorBatchSystem.GridEngineThread method) getEstimatedNodeCounts() (toil.provisioners.clusterScaler.ClusterScaler method) (toil.test.provisioners.clusterScalerTest.ClusterScaler method) getFileReaderCount() (toil.fileStores.cachingFileStore.CachingFileStore method) getFileSize() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) getFileSystemSize() (in module toil.common) (in module toil.fileStores.cachingFileStore) (in module toil.fileStores.nonCachingFileStore) getGlobalFileSize() (toil.batchSystems.abstractBatchSystem.AbstractFileStore method) (toil.cwl.cwltoil.AbstractFileStore method) (toil.cwl.utils.AbstractFileStore method) (toil.fileStores.abstractFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.AbstractFileStore method) (toil.fileStores.nonCachingFileStore.AbstractFileStore method) (toil.test.cwl.cwlTest.AbstractFileStore method) (toil.wdl.wdltoil.AbstractFileStore method) (toil.worker.AbstractFileStore method) getIssuedBatchJobIDs() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method) (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem method) (toil.batchSystems.awsBatch.AWSBatchBatchSystem method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem method) (toil.batchSystems.kubernetes.KubernetesBatchSystem method) (toil.batchSystems.local_support.SingleMachineBatchSystem method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem method) (toil.batchSystems.mesos.batchSystem.MesosBatchSystem method) (toil.batchSystems.singleMachine.SingleMachineBatchSystem method) (toil.batchSystems.slurm.AbstractGridEngineBatchSystem method) (toil.batchSystems.torque.AbstractGridEngineBatchSystem method) (toil.leader.AbstractBatchSystem method) (toil.provisioners.clusterScaler.AbstractBatchSystem method) (toil.test.batchSystems.batch_system_plugin_test.AbstractBatchSystem method) (toil.test.batchSystems.batch_system_plugin_test.FakeBatchSystem method) (toil.test.batchSystems.batchSystemTest.AbstractBatchSystem method) (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystem method) (toil.test.provisioners.clusterScalerTest.AbstractBatchSystem method) (toil.test.src.jobServiceTest.SingleMachineBatchSystem method) getIssuedLocalJobIDs() (toil.batchSystems.cleanup_support.BatchSystemLocalSupport method) (toil.batchSystems.local_support.BatchSystemLocalSupport method) (toil.batchSystems.mesos.batchSystem.BatchSystemLocalSupport method) getJobExitCode() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.gridengine.GridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.htcondor.HTCondorBatchSystem.GridEngineThread method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.lsf.LSFBatchSystem.GridEngineThread method) (toil.batchSystems.slurm.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.slurm.SlurmBatchSystem.GridEngineThread method) (toil.batchSystems.torque.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.torque.TorqueBatchSystem.GridEngineThread method) getJobExitCodeBACCT() (toil.batchSystems.lsf.LSFBatchSystem.GridEngineThread method) getJobs() (toil.leader.Leader method) (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method) getJobStore() (toil.batchSystems.abstractBatchSystem.Toil class method) (toil.batchSystems.awsBatch.Toil class method) (toil.batchSystems.cleanup_support.Toil class method) (toil.batchSystems.kubernetes.Toil class method) (toil.batchSystems.singleMachine.Toil class method) (toil.common.Toil class method) (toil.cwl.cwltoil.Toil class method) (toil.fileStores.abstractFileStore.Toil class method) (toil.job.Toil class method) (toil.server.wes.tasks.Toil class method) (toil.test.batchSystems.batch_system_plugin_test.Toil class method) (toil.test.batchSystems.batchSystemTest.Toil class method) (toil.test.jobStores.jobStoreTest.Toil class method) (toil.test.lib.dockerTest.Toil class method) (toil.test.mesos.helloWorld.Toil class method) (toil.test.options.options.Toil class method) (toil.test.sort.restart_sort.Toil class method) (toil.test.sort.sort.Toil class method) (toil.test.sort.sortTest.Toil class method) (toil.test.src.busTest.Toil class method) (toil.test.src.environmentTest.Toil class method) (toil.test.src.fileStoreTest.Toil class method) (toil.test.src.importExportFileTest.Toil class method) (toil.test.src.jobDescriptionTest.Toil class method) (toil.test.src.jobFileStoreTest.Toil class method) (toil.test.src.jobTest.Toil class method) (toil.test.src.restartDAGTest.Toil class method) (toil.test.src.toilContextManagerTest.Toil class method) (toil.test.utils.toilKillTest.Toil class method) (toil.test.utils.utilsTest.Toil class method) (toil.utils.toilClean.Toil class method) (toil.utils.toilDebugFile.Toil class method) (toil.utils.toilDebugJob.Toil class method) (toil.utils.toilKill.Toil class method) (toil.utils.toilStats.Toil class method) (toil.utils.toilStatus.Toil class method) (toil.wdl.wdltoil.Toil class method) (toil.worker.Toil class method) getKubernetesAutoscalerSetupCommands() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AWSProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.test.provisioners.aws.awsProvisionerTest.AWSProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) getKubernetesCloudProvider() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AWSProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.test.provisioners.aws.awsProvisionerTest.AWSProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) getKubernetesValues() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) getLeader() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AWSProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.provisioners.gceProvisioner.GCEProvisioner method) (toil.test.provisioners.aws.awsProvisionerTest.AWSProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method) getLocalTempDir() (toil.batchSystems.abstractBatchSystem.AbstractFileStore method) (toil.cwl.cwltoil.AbstractFileStore method) (toil.cwl.utils.AbstractFileStore method) (toil.fileStores.abstractFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.AbstractFileStore method) (toil.fileStores.nonCachingFileStore.AbstractFileStore method) (toil.test.cwl.cwlTest.AbstractFileStore method) (toil.wdl.wdltoil.AbstractFileStore method) (toil.worker.AbstractFileStore method) getLocalTempFile() (toil.batchSystems.abstractBatchSystem.AbstractFileStore method) (toil.cwl.cwltoil.AbstractFileStore method) (toil.cwl.utils.AbstractFileStore method) (toil.fileStores.abstractFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.AbstractFileStore method) (toil.fileStores.nonCachingFileStore.AbstractFileStore method) (toil.test.cwl.cwlTest.AbstractFileStore method) (toil.wdl.wdltoil.AbstractFileStore method) (toil.worker.AbstractFileStore method) getLocalTempFileName() (toil.batchSystems.abstractBatchSystem.AbstractFileStore method) (toil.cwl.cwltoil.AbstractFileStore method) (toil.cwl.utils.AbstractFileStore method) (toil.fileStores.abstractFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.AbstractFileStore method) (toil.fileStores.nonCachingFileStore.AbstractFileStore method) (toil.test.cwl.cwlTest.AbstractFileStore method) (toil.wdl.wdltoil.AbstractFileStore method) (toil.worker.AbstractFileStore method) getLocalWorkflowDir() (toil.batchSystems.abstractBatchSystem.Toil class method) (toil.batchSystems.awsBatch.Toil class method) (toil.batchSystems.cleanup_support.Toil class method) (toil.batchSystems.kubernetes.Toil class method) (toil.batchSystems.singleMachine.Toil class method) (toil.common.Toil class method) (toil.cwl.cwltoil.Toil class method) (toil.fileStores.abstractFileStore.Toil class method) (toil.job.Toil class method) (toil.server.wes.tasks.Toil class method) (toil.test.batchSystems.batch_system_plugin_test.Toil class method) (toil.test.batchSystems.batchSystemTest.Toil class method) (toil.test.jobStores.jobStoreTest.Toil class method) (toil.test.lib.dockerTest.Toil class method) (toil.test.mesos.helloWorld.Toil class method) (toil.test.options.options.Toil class method) (toil.test.sort.restart_sort.Toil class method) (toil.test.sort.sort.Toil class method) (toil.test.sort.sortTest.Toil class method) (toil.test.src.busTest.Toil class method) (toil.test.src.environmentTest.Toil class method) (toil.test.src.fileStoreTest.Toil class method) (toil.test.src.importExportFileTest.Toil class method) (toil.test.src.jobDescriptionTest.Toil class method) (toil.test.src.jobFileStoreTest.Toil class method) (toil.test.src.jobTest.Toil class method) (toil.test.src.restartDAGTest.Toil class method) (toil.test.src.toilContextManagerTest.Toil class method) (toil.test.utils.toilKillTest.Toil class method) (toil.test.utils.utilsTest.Toil class method) (toil.utils.toilClean.Toil class method) (toil.utils.toilDebugFile.Toil class method) (toil.utils.toilDebugJob.Toil class method) (toil.utils.toilKill.Toil class method) (toil.utils.toilStats.Toil class method) (toil.utils.toilStatus.Toil class method) (toil.wdl.wdltoil.Toil class method) (toil.worker.Toil class method) getLogFileHandle() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) getLogger() (toil.common.RealtimeLogger class method) (toil.deferred.RealtimeLogger class method) (toil.realtimeLogger.RealtimeLogger class method) (toil.test.sort.restart_sort.RealtimeLogger class method) (toil.test.sort.sort.RealtimeLogger class method) (toil.test.src.fileStoreTest.RealtimeLogger class method) (toil.test.src.realtimeLoggerTest.RealtimeLogger class method) getLogLevelString() (in module toil.lib.bioio) getMidPoint() (in module toil.test.sort.restart_sort) (in module toil.test.sort.sort) (in module toil.test.sort.sortTest) getNextJobID() (toil.batchSystems.cleanup_support.BatchSystemLocalSupport method) (toil.batchSystems.local_support.BatchSystemLocalSupport method) (toil.batchSystems.mesos.batchSystem.BatchSystemLocalSupport method) getNodeID() (in module toil.common) (in module toil.jobStores.abstractJobStore) (in module toil.test.src.miscTests) (in module toil.utils.toilKill) getNodes() (toil.batchSystems.abstractBatchSystem.AbstractScalableBatchSystem method) (toil.batchSystems.mesos.batchSystem.AbstractScalableBatchSystem method) (toil.batchSystems.mesos.batchSystem.MesosBatchSystem method) (toil.provisioners.clusterScaler.AbstractScalableBatchSystem method) (toil.provisioners.clusterScaler.ClusterScaler method) (toil.test.provisioners.clusterScalerTest.AbstractScalableBatchSystem method) (toil.test.provisioners.clusterScalerTest.ClusterScaler method) (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method) getNodeShape() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AWSProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.provisioners.gceProvisioner.GCEProvisioner method) (toil.test.provisioners.aws.awsProvisionerTest.AWSProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method) getNumberOfJobsIssued() (toil.leader.Leader method) (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method) getNumberOfNodes() (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method) getNumRetries() (toil.test.src.checkpointTest.CheckRetryCount method) getOne() (in module toil.test.src.promisedRequirementTest) getOptions() (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemJobTest method) (toil.test.batchSystems.batchSystemTest.MesosBatchSystemJobTest method) (toil.test.src.promisedRequirementTest.hidden.AbstractPromisedRequirementsTest method) (toil.test.src.promisedRequirementTest.MesosPromisedRequirementsTest method) getPIDStatus() (toil.test.utils.utilsTest.ToilStatus static method) (toil.utils.toilDebugJob.ToilStatus static method) (toil.utils.toilStatus.ToilStatus static method) getProvisionedWorkers() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AWSProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.provisioners.gceProvisioner.GCEProvisioner method) (toil.test.provisioners.aws.awsProvisionerTest.AWSProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method) getPublicUrl() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) getRandomEdge() (toil.test.src.jobTest.JobTest static method) getRequiredNodes() (toil.provisioners.clusterScaler.BinPackedFit method) (toil.test.provisioners.clusterScalerTest.BinPackedFit method) getRootJobReturnValue() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) getRootJobs() (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.Job method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) getRootVolID() (toil.test.provisioners.aws.awsProvisionerTest.AbstractAWSAutoscaleTest method) (toil.test.provisioners.aws.awsProvisionerTest.AWSAutoscaleTest method) getRunningBatchJobIDs() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method) (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem method) (toil.batchSystems.awsBatch.AWSBatchBatchSystem method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem method) (toil.batchSystems.kubernetes.KubernetesBatchSystem method) (toil.batchSystems.local_support.SingleMachineBatchSystem method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem method) (toil.batchSystems.mesos.batchSystem.MesosBatchSystem method) (toil.batchSystems.singleMachine.SingleMachineBatchSystem method) (toil.batchSystems.slurm.AbstractGridEngineBatchSystem method) (toil.batchSystems.torque.AbstractGridEngineBatchSystem method) (toil.leader.AbstractBatchSystem method) (toil.provisioners.clusterScaler.AbstractBatchSystem method) (toil.test.batchSystems.batch_system_plugin_test.AbstractBatchSystem method) (toil.test.batchSystems.batch_system_plugin_test.FakeBatchSystem method) (toil.test.batchSystems.batchSystemTest.AbstractBatchSystem method) (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystem method) (toil.test.provisioners.clusterScalerTest.AbstractBatchSystem method) (toil.test.src.jobServiceTest.SingleMachineBatchSystem method) getRunningJobIDs() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.gridengine.GridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.htcondor.HTCondorBatchSystem.GridEngineThread method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.lsf.LSFBatchSystem.GridEngineThread method) (toil.batchSystems.slurm.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.slurm.SlurmBatchSystem.GridEngineThread method) (toil.batchSystems.torque.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.torque.TorqueBatchSystem.GridEngineThread method) getRunningLocalJobIDs() (toil.batchSystems.cleanup_support.BatchSystemLocalSupport method) (toil.batchSystems.local_support.BatchSystemLocalSupport method) (toil.batchSystems.mesos.batchSystem.BatchSystemLocalSupport method) getSchedulingStatusMessage() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method) (toil.batchSystems.local_support.SingleMachineBatchSystem method) (toil.batchSystems.singleMachine.SingleMachineBatchSystem method) (toil.leader.AbstractBatchSystem method) (toil.provisioners.clusterScaler.AbstractBatchSystem method) (toil.test.batchSystems.batch_system_plugin_test.AbstractBatchSystem method) (toil.test.batchSystems.batchSystemTest.AbstractBatchSystem method) (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystem method) (toil.test.provisioners.clusterScalerTest.AbstractBatchSystem method) (toil.test.src.jobServiceTest.SingleMachineBatchSystem method) getSharedPublicUrl() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) getSize() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo method) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo method) getSpaceUsableForJobs() (toil.fileStores.cachingFileStore.CachingFileStore method) getStaticNodes() (toil.provisioners.clusterScaler.ClusterScaler method) (toil.test.provisioners.clusterScalerTest.ClusterScaler method) getStatus() (toil.test.utils.utilsTest.ToilStatus static method) (toil.utils.toilDebugJob.ToilStatus static method) (toil.utils.toilStatus.ToilStatus static method) getSuccessors() (toil.leader.Leader method) getTempFile() (in module toil.lib.bioio) getThirtyTwoMb() (in module toil.test.src.promisedRequirementTest) getToilWorkDir() (toil.batchSystems.abstractBatchSystem.Toil static method) (toil.batchSystems.awsBatch.Toil static method) (toil.batchSystems.cleanup_support.Toil static method) (toil.batchSystems.kubernetes.Toil static method) (toil.batchSystems.singleMachine.Toil static method) (toil.common.Toil static method) (toil.cwl.cwltoil.Toil static method) (toil.fileStores.abstractFileStore.Toil static method) (toil.job.Toil static method) (toil.server.wes.tasks.Toil static method) (toil.test.batchSystems.batch_system_plugin_test.Toil static method) (toil.test.batchSystems.batchSystemTest.Toil static method) (toil.test.jobStores.jobStoreTest.Toil static method) (toil.test.lib.dockerTest.Toil static method) (toil.test.mesos.helloWorld.Toil static method) (toil.test.options.options.Toil static method) (toil.test.sort.restart_sort.Toil static method) (toil.test.sort.sort.Toil static method) (toil.test.sort.sortTest.Toil static method) (toil.test.src.busTest.Toil static method) (toil.test.src.environmentTest.Toil static method) (toil.test.src.fileStoreTest.Toil static method) (toil.test.src.importExportFileTest.Toil static method) (toil.test.src.jobDescriptionTest.Toil static method) (toil.test.src.jobFileStoreTest.Toil static method) (toil.test.src.jobTest.Toil static method) (toil.test.src.restartDAGTest.Toil static method) (toil.test.src.toilContextManagerTest.Toil static method) (toil.test.utils.toilKillTest.Toil static method) (toil.test.utils.utilsTest.Toil static method) (toil.utils.toilClean.Toil static method) (toil.utils.toilDebugFile.Toil static method) (toil.utils.toilDebugJob.Toil static method) (toil.utils.toilKill.Toil static method) (toil.utils.toilStats.Toil static method) (toil.utils.toilStatus.Toil static method) (toil.wdl.wdltoil.Toil static method) (toil.worker.Toil static method) getTopologicalOrderingOfJobs() (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.Job method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) getUpdatedBatchJob() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method) (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem method) (toil.batchSystems.awsBatch.AWSBatchBatchSystem method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem method) (toil.batchSystems.kubernetes.KubernetesBatchSystem method) (toil.batchSystems.local_support.SingleMachineBatchSystem method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem method) (toil.batchSystems.mesos.batchSystem.MesosBatchSystem method) (toil.batchSystems.singleMachine.SingleMachineBatchSystem method) (toil.batchSystems.slurm.AbstractGridEngineBatchSystem method) (toil.batchSystems.torque.AbstractGridEngineBatchSystem method) (toil.batchSystems.torque.TorqueBatchSystem.GridEngineThread method) (toil.leader.AbstractBatchSystem method) (toil.provisioners.clusterScaler.AbstractBatchSystem method) (toil.test.batchSystems.batch_system_plugin_test.AbstractBatchSystem method) (toil.test.batchSystems.batch_system_plugin_test.FakeBatchSystem method) (toil.test.batchSystems.batchSystemTest.AbstractBatchSystem method) (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystem method) (toil.test.provisioners.clusterScalerTest.AbstractBatchSystem method) (toil.test.src.jobServiceTest.SingleMachineBatchSystem method) getUpdatedLocalJob() (toil.batchSystems.cleanup_support.BatchSystemLocalSupport method) (toil.batchSystems.local_support.BatchSystemLocalSupport method) (toil.batchSystems.mesos.batchSystem.BatchSystemLocalSupport method) getUserScript() (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.EncapsulatedJob method) (toil.job.FunctionWrappingJob method) (toil.job.Job method) (toil.job.ServiceHostJob method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) getValue() (toil.job.PromisedRequirement method) (toil.test.src.promisedRequirementTest.PromisedRequirement method) getWaitDuration() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem class method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem class method) (toil.batchSystems.gridengine.GridEngineBatchSystem class method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem class method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem class method) (toil.batchSystems.lsf.LSFBatchSystem method) 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(toil.test.provisioners.clusterScalerTest.AbstractBatchSystem method) getWorkersInCluster() (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method) glob() (in module toil.lib.resources) (in module toil.test.utils.toilDebugTest) (in module toil.utils.toilDebugFile) (toil.cwl.cwltoil.ToilFsAccess method) global_mutex() (in module toil.lib.threading) (in module toil.server.wes.toil_backend) (in module toil.test.src.threadingTest) (in module toil.wdl.wdltoil) globalize() (toil.deferred.ModuleDescriptor method) (toil.job.ModuleDescriptor method) (toil.resource.ModuleDescriptor method) (toil.test.src.jobDescriptionTest.ModuleDescriptor method) (toil.test.src.resourceTest.ModuleDescriptor method) goodChild() (in module toil.test.src.resumabilityTest) google_retry() (in module toil.jobStores.googleJobStore) (in module toil.test.jobStores.jobStoreTest) google_retry_predicate() (in module toil.jobStores.googleJobStore) GOOGLE_STORAGE (in module toil.jobStores.googleJobStore) GoogleJobStore (class in toil.jobStores.googleJobStore) (class in toil.provisioners.gceProvisioner) GoogleJobStoreTest (class in toil.test.jobStores.jobStoreTest) grandChildJob() (in module toil.test.batchSystems.batchSystemTest) greater_than() (toil.batchSystems.mesos.Shape method) (toil.provisioners.abstractProvisioner.Shape method) (toil.provisioners.aws.awsProvisioner.Shape method) (toil.provisioners.clusterScaler.Shape method) (toil.provisioners.gceProvisioner.Shape method) (toil.test.provisioners.clusterScalerTest.Shape method) greatGrandChild() (in module toil.test.batchSystems.batchSystemTest) gridengine_batch_system_factory() (in module toil.batchSystems.registry) GridEngineBatchSystem (class in toil.batchSystems.gridengine) GridEngineBatchSystem.GridEngineThread (class in toil.batchSystems.gridengine) GridEngineBatchSystemTest (class in toil.test.batchSystems.batchSystemTest) GunicornApplication (class in toil.server.wsgi_app)

H

h2b() (in module toil.lib.humanize) (in module toil.test.provisioners.clusterScalerTest) handle() (toil.realtimeLogger.LoggingDatagramHandler method) handle_errors() (in module toil.server.wes.abstract_backend) (in module toil.server.wes.toil_backend) handle_injection_messages() (toil.wdl.wdltoil.WDLTaskJob method) handle_message_file() (toil.wdl.wdltoil.WDLTaskJob method) handleLocalJob() (toil.batchSystems.cleanup_support.BatchSystemLocalSupport method) (toil.batchSystems.local_support.BatchSystemLocalSupport method) (toil.batchSystems.mesos.batchSystem.BatchSystemLocalSupport method) has_body() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) 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toil.test.src.promisedRequirementTest) hidden.AbstractStateStoreTest (class in toil.test.server.serverTest) hms_duration_to_seconds() (in module toil.batchSystems.torque) (in module toil.lib.conversions) (in module toil.test.lib.test_conversions) htcondor_batch_system_factory() (in module toil.batchSystems.registry) HTCondorBatchSystem (class in toil.batchSystems.htcondor) HTCondorBatchSystem.GridEngineThread (class in toil.batchSystems.htcondor) HTCondorBatchSystemTest (class in toil.test.batchSystems.batchSystemTest) human2bytes() (in module toil.batchSystems.kubernetes) (in module toil.job) (in module toil.lib.conversions) (in module toil.lib.humanize) (in module toil.options.common) (in module toil.provisioners.aws.awsProvisioner) (in module toil.provisioners.clusterScaler) (in module toil.provisioners.gceProvisioner) (in module toil.test.lib.test_conversions) (in module toil.wdl.wdltoil)

I

iam_client (in module toil.lib.ec2) IAMTest (class in toil.test.lib.aws.test_iam) iC() (in module toil.options.common) ignoreNode() (toil.batchSystems.abstractBatchSystem.AbstractScalableBatchSystem method) (toil.batchSystems.mesos.batchSystem.AbstractScalableBatchSystem method) (toil.batchSystems.mesos.batchSystem.MesosBatchSystem method) (toil.provisioners.clusterScaler.AbstractScalableBatchSystem method) (toil.test.provisioners.clusterScalerTest.AbstractScalableBatchSystem method) (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method) IllegalDeletionCacheError, [1] import_file() (toil.batchSystems.abstractBatchSystem.AbstractFileStore method) (toil.batchSystems.abstractBatchSystem.Toil method) (toil.batchSystems.awsBatch.Toil method) (toil.batchSystems.cleanup_support.Toil method) (toil.batchSystems.kubernetes.Toil method) (toil.batchSystems.singleMachine.Toil method) (toil.common.Toil method) (toil.cwl.cwltoil.AbstractFileStore method) 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(toil.utils.toilStats.AbstractJobStore method) (toil.utils.toilStats.Toil method) (toil.utils.toilStatus.Toil method) (toil.wdl.wdltoil.AbstractFileStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.wdl.wdltoil.Toil method) (toil.worker.AbstractFileStore method) (toil.worker.AbstractJobStore method) (toil.worker.Toil method) in_contexts() (in module toil.worker) inconsistencies_detected() (in module toil.lib.ec2) INCONSISTENCY_ERRORS (in module toil.lib.ec2) increase_instance_hop_limit() (in module toil.lib.ec2) (in module toil.provisioners.aws.awsProvisioner) Info (class in toil.batchSystems.singleMachine) init() (toil.server.wsgi_app.GunicornApplication method) init_action_collection() (in module toil.lib.aws.iam) initialize() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method)

initialize_run() (toil.server.wes.tasks.ToilWorkflowRunner method) initialized (toil.common.RealtimeLogger attribute) (toil.deferred.RealtimeLogger attribute) (toil.realtimeLogger.RealtimeLogger attribute) (toil.test.sort.restart_sort.RealtimeLogger attribute) (toil.test.sort.sort.RealtimeLogger attribute) (toil.test.src.fileStoreTest.RealtimeLogger attribute) (toil.test.src.realtimeLoggerTest.RealtimeLogger attribute) INJECTED_MESSAGE_DIR (toil.wdl.wdltoil.WDLTaskJob attribute) injectFile() (toil.provisioners.abstractProvisioner.Node method) (toil.provisioners.aws.awsProvisioner.Node method) (toil.provisioners.gceProvisioner.Node method) (toil.provisioners.node.Node method) (toil.test.provisioners.clusterScalerTest.Node method) InnerClass (class in toil.jobStores.aws.jobStore) (class in toil.lib.objects) innerLoop() (toil.leader.Leader method) insertJob() (toil.batchSystems.mesos.batchSystem.JobQueue method) (toil.batchSystems.mesos.JobQueue method) install_log_color() (in module toil.statsAndLogging) (in module toil.worker) instance_type (toil.bus.ClusterDesiredSizeMessage attribute) (toil.bus.ClusterSizeMessage attribute) (toil.common.ClusterDesiredSizeMessage attribute) (toil.common.ClusterSizeMessage attribute) (toil.provisioners.clusterScaler.ClusterDesiredSizeMessage attribute) (toil.provisioners.clusterScaler.ClusterSizeMessage attribute) InstanceType (class in toil.lib.ec2nodes) (class in toil.lib.generatedEC2Lists) (class in toil.provisioners.aws.awsProvisioner) InsufficientSystemResources, [1], [2], [3], [4], [5], [6], [7] integrative() (in module toil.test) (in module toil.test.provisioners.aws.awsProvisionerTest) (in module toil.test.provisioners.gceProvisionerTest) (in module toil.test.utils.utilsTest) (in module toil.test.wdl.wdltoil_test) (in module toil.test.wdl.wdltoil_test_kubernetes) internet_connection() (in module toil.utils.toilUpdateEC2Instances) InvalidAWSJobStoreTest (class in toil.test.jobStores.jobStoreTest) InvalidClusterStateException InvalidImportExportUrlException, [1], [2] InvalidRequestError InvalidSourceCacheError inVirtualEnv() (in module toil) (in module toil.resource) (in module toil.test.src.resourceTest) invoke() (toil.deferred.DeferredFunction method) (toil.job.DeferredFunction method) is_active() (toil.leader.ServiceManager method) (toil.serviceManager.ServiceManager method) is_decl() (toil.test.wdl.wdltoil_test.WDLWorkflowGraph method) (toil.wdl.wdltoil.WDLWorkflowGraph method) is_false() (toil.cwl.cwltoil.Conditional method) is_number() (in module toil.lib.ec2nodes) is_ok() (toil.server.wes.tasks.MultiprocessingTaskRunner class method) (toil.server.wes.tasks.TaskRunner static method) (toil.server.wes.toil_backend.MultiprocessingTaskRunner class method) (toil.server.wes.toil_backend.TaskRunner static method) is_retryable_kubernetes_error() (in module toil.batchSystems.kubernetes) is_running() (toil.leader.ServiceManager method) (toil.serviceManager.ServiceManager method) is_subtree_done() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) is_updated_by() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) is_url() (in module toil.wdl.wdltoil) isAcyclic() (toil.test.src.jobTest.JobTest method) isdir() (toil.cwl.cwltoil.ToilFsAccess method) isfile() (toil.cwl.cwltoil.ToilFsAccess method) issueBatchJob() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method) (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem method) (toil.batchSystems.awsBatch.AWSBatchBatchSystem method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem method) (toil.batchSystems.htcondor.HTCondorBatchSystem method) (toil.batchSystems.kubernetes.KubernetesBatchSystem method) (toil.batchSystems.local_support.SingleMachineBatchSystem method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem method) (toil.batchSystems.mesos.batchSystem.MesosBatchSystem method) (toil.batchSystems.singleMachine.SingleMachineBatchSystem method) (toil.batchSystems.slurm.AbstractGridEngineBatchSystem method) (toil.batchSystems.torque.AbstractGridEngineBatchSystem method) (toil.leader.AbstractBatchSystem method) (toil.provisioners.clusterScaler.AbstractBatchSystem method) (toil.test.batchSystems.batch_system_plugin_test.AbstractBatchSystem method) (toil.test.batchSystems.batch_system_plugin_test.FakeBatchSystem method) (toil.test.batchSystems.batchSystemTest.AbstractBatchSystem method) (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystem method) (toil.test.provisioners.clusterScalerTest.AbstractBatchSystem method) (toil.test.src.jobServiceTest.SingleMachineBatchSystem method) issueJob() (toil.leader.Leader method) issueJobs() (toil.leader.Leader method) issueQueingServiceJobs() (toil.leader.Leader method) issueServiceJob() (toil.leader.Leader method) IT (in module toil.lib.iterables) itemsPerBatchDelete (toil.jobStores.aws.jobStore.AWSJobStore attribute) (toil.test.lib.aws.test_s3.AWSJobStore attribute) ItemT (toil.batchSystems.kubernetes.KubernetesBatchSystem attribute)

J

Job (class in toil.cwl.cwltoil) (class in toil.fileStores.abstractFileStore) (class in toil.fileStores.cachingFileStore) (class in toil.fileStores.nonCachingFileStore) (class in toil.job) (class in toil.jobStores.aws.jobStore) (class in toil.test.batchSystems.batchSystemTest) (class in toil.test.jobStores.jobStoreTest) (class in toil.test.lib.dockerTest) (class in toil.test.mesos.helloWorld) (class in toil.test.mesos.stress) (class in toil.test.provisioners.restartScript) (class in toil.test.sort.restart_sort) (class in toil.test.sort.sort) (class in toil.test.sort.sortTest) (class in toil.test.src.busTest) (class in toil.test.src.checkpointTest) (class in toil.test.src.deferredFunctionTest) (class in toil.test.src.environmentTest) (class in toil.test.src.fileStoreTest) (class in toil.test.src.helloWorldTest) (class in toil.test.src.importExportFileTest) (class in toil.test.src.jobDescriptionTest) (class in toil.test.src.jobEncapsulationTest) (class in toil.test.src.jobFileStoreTest) (class in toil.test.src.jobServiceTest) (class in toil.test.src.jobTest) (class in toil.test.src.promisedRequirementTest) (class in toil.test.src.promisesTest) (class in toil.test.src.realtimeLoggerTest) (class in toil.test.src.restartDAGTest) (class in toil.test.src.resumabilityTest) (class in toil.test.src.retainTempDirTest) (class in toil.test.src.toilContextManagerTest) (class in toil.test.src.userDefinedJobArgTypeTest) (class in toil.test.utils.utilsTest) (class in toil.utils.toilStats) (class in toil.wdl.wdltoil) (class in toil.worker) Job.Runner (class in toil.cwl.cwltoil) (class in toil.fileStores.abstractFileStore) (class in toil.fileStores.cachingFileStore) (class in toil.fileStores.nonCachingFileStore) (class in toil.job) (class in toil.jobStores.aws.jobStore) (class in toil.test.batchSystems.batchSystemTest) (class in toil.test.jobStores.jobStoreTest) (class in toil.test.lib.dockerTest) (class in toil.test.mesos.helloWorld) (class in toil.test.mesos.stress) (class in toil.test.provisioners.restartScript) (class in toil.test.sort.restart_sort) (class in toil.test.sort.sort) (class in toil.test.sort.sortTest) (class in toil.test.src.busTest) (class in toil.test.src.checkpointTest) (class in toil.test.src.deferredFunctionTest) (class in toil.test.src.environmentTest) (class in toil.test.src.fileStoreTest) (class in toil.test.src.helloWorldTest) (class in toil.test.src.importExportFileTest) (class in toil.test.src.jobDescriptionTest) (class in toil.test.src.jobEncapsulationTest) (class in toil.test.src.jobFileStoreTest) (class in toil.test.src.jobServiceTest) (class in toil.test.src.jobTest) (class in toil.test.src.promisedRequirementTest) (class in toil.test.src.promisesTest) (class in toil.test.src.realtimeLoggerTest) (class in toil.test.src.restartDAGTest) (class in toil.test.src.resumabilityTest) (class in toil.test.src.retainTempDirTest) (class in toil.test.src.toilContextManagerTest) (class in toil.test.src.userDefinedJobArgTypeTest) (class in toil.test.utils.utilsTest) (class in toil.utils.toilStats) (class in toil.wdl.wdltoil) (class in toil.worker) Job.Service (class in toil.cwl.cwltoil) (class in toil.fileStores.abstractFileStore) (class in toil.fileStores.cachingFileStore) (class in toil.fileStores.nonCachingFileStore) (class in toil.job) (class in toil.jobStores.aws.jobStore) (class in toil.test.batchSystems.batchSystemTest) (class in toil.test.jobStores.jobStoreTest) (class in toil.test.lib.dockerTest) (class in toil.test.mesos.helloWorld) (class in toil.test.mesos.stress) (class in toil.test.provisioners.restartScript) (class in toil.test.sort.restart_sort) (class in toil.test.sort.sort) (class in toil.test.sort.sortTest) (class in toil.test.src.busTest) (class in toil.test.src.checkpointTest) (class in toil.test.src.deferredFunctionTest) (class in toil.test.src.environmentTest) (class in toil.test.src.fileStoreTest) (class in toil.test.src.helloWorldTest) (class in toil.test.src.importExportFileTest) (class in toil.test.src.jobDescriptionTest) (class in toil.test.src.jobEncapsulationTest) (class in toil.test.src.jobFileStoreTest) (class in toil.test.src.jobServiceTest) (class in toil.test.src.jobTest) (class in toil.test.src.promisedRequirementTest) (class in toil.test.src.promisesTest) (class in toil.test.src.realtimeLoggerTest) (class in toil.test.src.restartDAGTest) (class in toil.test.src.resumabilityTest) (class in toil.test.src.retainTempDirTest) (class in toil.test.src.toilContextManagerTest) (class in toil.test.src.userDefinedJobArgTypeTest) (class in toil.test.utils.utilsTest) (class in toil.utils.toilStats) (class in toil.wdl.wdltoil) (class in toil.worker) JOB_DIR_PREFIX (toil.cwl.cwltoil.FileJobStore attribute) (toil.jobStores.fileJobStore.FileJobStore attribute) (toil.test.jobStores.jobStoreTest.FileJobStore attribute) (toil.test.src.workerTest.FileJobStore attribute) (toil.utils.toilDebugFile.FileJobStore attribute) (toil.utils.toilDebugJob.FileJobStore attribute) job_exists() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.leader.ToilState method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.serviceManager.ToilState method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.toilState.ToilState method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) job_id (toil.bus.JobAnnotationMessage attribute) (toil.bus.JobCompletedMessage attribute) (toil.bus.JobFailedMessage attribute) (toil.bus.JobIssuedMessage attribute) (toil.bus.JobMissingMessage attribute) (toil.bus.JobUpdatedMessage attribute) (toil.common.JobCompletedMessage attribute) (toil.common.JobFailedMessage attribute) (toil.common.JobIssuedMessage attribute) (toil.common.JobMissingMessage attribute) (toil.leader.JobCompletedMessage attribute) (toil.leader.JobFailedMessage attribute) (toil.leader.JobIssuedMessage attribute) (toil.leader.JobMissingMessage attribute) (toil.leader.JobUpdatedMessage attribute) (toil.test.src.busTest.JobCompletedMessage attribute) (toil.test.src.busTest.JobIssuedMessage attribute) (toil.toilState.JobUpdatedMessage attribute) job_name (toil.bus.Names attribute) (toil.job.Names attribute) JOB_NAME_DIR_PREFIX (toil.cwl.cwltoil.FileJobStore attribute) (toil.jobStores.fileJobStore.FileJobStore attribute) (toil.test.jobStores.jobStoreTest.FileJobStore attribute) (toil.test.src.workerTest.FileJobStore attribute) (toil.utils.toilDebugFile.FileJobStore attribute) (toil.utils.toilDebugJob.FileJobStore attribute) job_store_id (toil.bus.JobStatus attribute) (toil.bus.Names attribute) (toil.job.Names attribute) (toil.server.wes.amazon_wes_utils.JobStatus attribute) (toil.server.wes.toil_backend.JobStatus attribute) job_store_timeout (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute)

job_type (toil.bus.JobCompletedMessage attribute) (toil.bus.JobFailedMessage attribute) (toil.bus.JobIssuedMessage attribute) (toil.common.JobCompletedMessage attribute) (toil.common.JobFailedMessage attribute) (toil.common.JobIssuedMessage attribute) (toil.leader.JobCompletedMessage attribute) (toil.leader.JobFailedMessage attribute) (toil.leader.JobIssuedMessage attribute) (toil.test.src.busTest.JobCompletedMessage attribute) (toil.test.src.busTest.JobIssuedMessage attribute) JobAnnotationMessage (class in toil.bus) JobBodyReference (class in toil.job) JobClass (class in toil.test.src.userDefinedJobArgTypeTest) JobCompletedMessage (class in toil.bus) (class in toil.common) (class in toil.leader) (class in toil.test.src.busTest) JobDescription (class in toil.batchSystems.abstractBatchSystem) (class in toil.batchSystems.awsBatch) (class in toil.batchSystems.kubernetes) (class in toil.batchSystems.local_support) (class in toil.batchSystems.mesos.batchSystem) (class in toil.batchSystems.singleMachine) (class in toil.fileStores.abstractFileStore) (class in toil.fileStores.cachingFileStore) (class in toil.fileStores.nonCachingFileStore) (class in toil.job) (class in toil.jobStores.abstractJobStore) (class in toil.jobStores.aws.jobStore) (class in toil.leader) (class in toil.provisioners.clusterScaler) (class in toil.test.batchSystems.batch_system_plugin_test) (class in toil.test.batchSystems.batchSystemTest) (class in toil.test.jobStores.jobStoreTest) (class in toil.test.provisioners.clusterScalerTest) (class in toil.test.src.jobDescriptionTest) (class in toil.test.src.workerTest) (class in toil.toilState) (class in toil.utils.toilStatus) (class in toil.worker) JobDescriptionTest (class in toil.test.src.jobDescriptionTest) JobEncapsulationTest (class in toil.test.src.jobEncapsulationTest) JobException, [1], [2] JobFailedMessage (class in toil.bus) (class in toil.common) (class in toil.leader) JobFileStoreTest (class in toil.test.src.jobFileStoreTest) jobFunction() (in module toil.test.src.userDefinedJobArgTypeTest) JobFunctionWrappingJob (class in toil.job) (class in toil.test.src.jobTest) JobGraphDeadlockException, [1] jobID (toil.batchSystems.abstractBatchSystem.UpdatedBatchJobInfo attribute) (toil.batchSystems.abstractGridEngineBatchSystem.UpdatedBatchJobInfo attribute) (toil.batchSystems.awsBatch.UpdatedBatchJobInfo attribute) (toil.batchSystems.kubernetes.UpdatedBatchJobInfo attribute) (toil.batchSystems.local_support.UpdatedBatchJobInfo attribute) (toil.batchSystems.mesos.batchSystem.UpdatedBatchJobInfo attribute) (toil.batchSystems.singleMachine.UpdatedBatchJobInfo attribute) (toil.batchSystems.torque.UpdatedBatchJobInfo attribute) (toil.test.batchSystems.batch_system_plugin_test.UpdatedBatchJobInfo attribute) jobIDs() (toil.batchSystems.mesos.batchSystem.JobQueue method) (toil.batchSystems.mesos.JobQueue method) JobIssuedMessage (class in toil.bus) (class in toil.common) (class in toil.leader) (class in toil.test.src.busTest) JobMissingMessage (class in toil.bus) (class in toil.common) (class in toil.leader) JobPromiseConstraintError JobQueue (class in toil.batchSystems.mesos) (class in toil.batchSystems.mesos.batchSystem) jobs (toil.worker.StatsDict attribute) jobs() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) JobServiceTest (class in toil.test.src.jobServiceTest) jobsPerBatchInsert (toil.jobStores.aws.jobStore.AWSJobStore attribute) (toil.test.lib.aws.test_s3.AWSJobStore attribute) JobStatus (class in toil.bus) (class in toil.server.wes.amazon_wes_utils) (class in toil.server.wes.toil_backend) jobStore (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) JOBSTORE_HELP (in module toil.common) (in module toil.options.common) JobStoreExistsException, [1], [2], [3], [4] jobStoreID (toil.cwl.cwltoil.Job property) (toil.fileStores.abstractFileStore.Job property) (toil.fileStores.cachingFileStore.Job property) (toil.fileStores.nonCachingFileStore.Job property) (toil.job.Job property) (toil.jobStores.aws.jobStore.Job property) (toil.test.batchSystems.batchSystemTest.Job property) (toil.test.jobStores.jobStoreTest.Job property) (toil.test.lib.dockerTest.Job property) (toil.test.mesos.helloWorld.Job property) (toil.test.mesos.stress.Job property) (toil.test.provisioners.restartScript.Job property) (toil.test.sort.restart_sort.Job property) (toil.test.sort.sort.Job property) (toil.test.sort.sortTest.Job property) (toil.test.src.busTest.Job property) (toil.test.src.checkpointTest.Job property) (toil.test.src.deferredFunctionTest.Job property) (toil.test.src.environmentTest.Job property) (toil.test.src.fileStoreTest.Job property) (toil.test.src.helloWorldTest.Job property) (toil.test.src.importExportFileTest.Job property) (toil.test.src.jobDescriptionTest.Job property) (toil.test.src.jobEncapsulationTest.Job property) (toil.test.src.jobFileStoreTest.Job property) (toil.test.src.jobServiceTest.Job property) (toil.test.src.jobTest.Job property) (toil.test.src.promisedRequirementTest.Job property) (toil.test.src.promisesTest.Job property) (toil.test.src.realtimeLoggerTest.Job property) (toil.test.src.restartDAGTest.Job property) (toil.test.src.resumabilityTest.Job property) (toil.test.src.retainTempDirTest.Job property) (toil.test.src.toilContextManagerTest.Job property) (toil.test.src.userDefinedJobArgTypeTest.Job property) (toil.test.utils.utilsTest.Job property) (toil.utils.toilStats.Job property) (toil.wdl.wdltoil.Job property) (toil.worker.Job property) JobStoreSupport (class in toil.jobStores.abstractJobStore) jobStoreType (toil.test.src.deferredFunctionTest.DeferredFunctionTest attribute) (toil.test.src.fileStoreTest.CachingFileStoreTestWithAwsJobStore attribute) (toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore attribute) (toil.test.src.fileStoreTest.CachingFileStoreTestWithGoogleJobStore attribute) (toil.test.src.fileStoreTest.hidden.AbstractFileStoreTest attribute) (toil.test.src.fileStoreTest.NonCachingFileStoreTestWithAwsJobStore attribute) (toil.test.src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore attribute) (toil.test.src.fileStoreTest.NonCachingFileStoreTestWithGoogleJobStore attribute) JobStoreUnavailableException, [1] JobTest (class in toil.test.src.jobTest) JobTooBigError, [1], [2] JobTuple (in module toil.batchSystems.abstractGridEngineBatchSystem) (in module toil.batchSystems.htcondor) JobUpdatedMessage (class in toil.bus) (class in toil.leader) (class in toil.toilState) join() (toil.batchSystems.mesos.test.ExceptionalThread method) (toil.cwl.cwltoil.ExceptionalThread method) (toil.cwl.cwltoil.ToilFsAccess method) (toil.jobStores.utils.ExceptionalThread method) (toil.lib.threading.ExceptionalThread method) (toil.provisioners.clusterScaler.ExceptionalThread method) (toil.test.ExceptionalThread method) JSONDatagramHandler (class in toil.realtimeLogger) JustAValue (class in toil.cwl.cwltoil)

K

KeyValuesList (in module toil.batchSystems.kubernetes) kill_polling_interval (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) kill_services() (toil.leader.ServiceManager method) (toil.serviceManager.ServiceManager method) killBatchJobs() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method) (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem method) (toil.batchSystems.awsBatch.AWSBatchBatchSystem method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem method) (toil.batchSystems.kubernetes.KubernetesBatchSystem method) (toil.batchSystems.local_support.SingleMachineBatchSystem method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem method) (toil.batchSystems.mesos.batchSystem.MesosBatchSystem method) (toil.batchSystems.singleMachine.SingleMachineBatchSystem method) (toil.batchSystems.slurm.AbstractGridEngineBatchSystem method) (toil.batchSystems.torque.AbstractGridEngineBatchSystem method) (toil.leader.AbstractBatchSystem method) (toil.provisioners.clusterScaler.AbstractBatchSystem method) (toil.test.batchSystems.batch_system_plugin_test.AbstractBatchSystem method) (toil.test.batchSystems.batch_system_plugin_test.FakeBatchSystem method) (toil.test.batchSystems.batchSystemTest.AbstractBatchSystem method) (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystem method) (toil.test.provisioners.clusterScalerTest.AbstractBatchSystem method) (toil.test.src.jobServiceTest.SingleMachineBatchSystem method) KILLED (toil.batchSystems.abstractBatchSystem.BatchJobExitReason attribute) (toil.batchSystems.abstractGridEngineBatchSystem.BatchJobExitReason attribute) (toil.batchSystems.awsBatch.BatchJobExitReason attribute) (toil.batchSystems.kubernetes.BatchJobExitReason attribute) (toil.batchSystems.lsf.BatchJobExitReason attribute) (toil.batchSystems.mesos.batchSystem.BatchJobExitReason attribute) (toil.batchSystems.slurm.BatchJobExitReason attribute) (toil.leader.BatchJobExitReason attribute) (toil.test.batchSystems.test_slurm.BatchJobExitReason attribute) (toil.test.src.busTest.BatchJobExitReason attribute) killJob() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.gridengine.GridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.htcondor.HTCondorBatchSystem.GridEngineThread method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.lsf.LSFBatchSystem.GridEngineThread method) (toil.batchSystems.slurm.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.slurm.SlurmBatchSystem.GridEngineThread method) (toil.batchSystems.torque.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.torque.TorqueBatchSystem.GridEngineThread method) killJobs() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.slurm.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.torque.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.leader.Leader method) killLocalJobs() (toil.batchSystems.cleanup_support.BatchSystemLocalSupport method) (toil.batchSystems.local_support.BatchSystemLocalSupport method) (toil.batchSystems.mesos.batchSystem.BatchSystemLocalSupport method) killTask() (toil.batchSystems.mesos.executor.MesosExecutor method) kind (toil.batchSystems.abstractGridEngineBatchSystem.AcceleratorRequirement attribute) (toil.batchSystems.htcondor.AcceleratorRequirement attribute) (toil.batchSystems.singleMachine.AcceleratorRequirement attribute) (toil.cwl.cwltoil.AcceleratorRequirement attribute) (toil.job.AcceleratorRequirement attribute) (toil.lib.accelerators.AcceleratorRequirement attribute) (toil.wdl.wdltoil.AcceleratorRequirement attribute) KNOWN_EXTANT_IMAGES (in module toil) kubernetes (in module toil.lib.retry) kubernetes_batch_system_factory() (in module toil.batchSystems.registry) kubernetes_host_path (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.kubernetes.KubernetesBatchSystem.KubernetesConfig attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute)

kubernetes_owner (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.kubernetes.KubernetesBatchSystem.KubernetesConfig attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) kubernetes_pod_timeout (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.kubernetes.KubernetesBatchSystem.KubernetesConfig attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) kubernetes_policy() (toil.provisioners.aws.awsProvisioner.AWSProvisioner method) (toil.test.provisioners.aws.awsProvisionerTest.AWSProvisioner method) kubernetes_privileged (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) kubernetes_service_account (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.kubernetes.KubernetesBatchSystem.KubernetesConfig attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) KubernetesBatchSystem (class in toil.batchSystems.kubernetes) KubernetesBatchSystem.DecoratorWrapper (class in toil.batchSystems.kubernetes) KubernetesBatchSystem.KubernetesConfig (class in toil.batchSystems.kubernetes) KubernetesBatchSystem.Placement (class in toil.batchSystems.kubernetes) KubernetesBatchSystemBenchTest (class in toil.test.batchSystems.batchSystemTest) KubernetesBatchSystemTest (class in toil.test.batchSystems.batchSystemTest)

L

LastProcessStandingArena (class in toil.batchSystems.cleanup_support) (class in toil.lib.threading) (class in toil.test.src.threadingTest) launchCluster() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AWSProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.provisioners.gceProvisioner.GCEProvisioner method) (toil.test.cactus.test_cactus_integration.AbstractClusterTest method) (toil.test.provisioners.aws.awsProvisionerTest.AbstractClusterTest method) (toil.test.provisioners.aws.awsProvisionerTest.AWSAutoscaleTest method) (toil.test.provisioners.aws.awsProvisionerTest.AWSManagedAutoscaleTest method) (toil.test.provisioners.aws.awsProvisionerTest.AWSProvisioner method) (toil.test.provisioners.aws.awsProvisionerTest.AWSStaticAutoscaleTest method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method) (toil.test.provisioners.clusterTest.AbstractClusterTest method) (toil.test.provisioners.gceProvisionerTest.AbstractGCEAutoscaleTest method) (toil.test.provisioners.gceProvisionerTest.GCEAutoscaleTest method) (toil.test.provisioners.gceProvisionerTest.GCEStaticAutoscaleTest method) (toil.test.wdl.wdltoil_test_kubernetes.AbstractClusterTest method) (toil.test.wdl.wdltoil_test_kubernetes.WDLKubernetesClusterTest method) launchTask() (toil.batchSystems.mesos.executor.MesosExecutor method) Leader (class in toil.leader) LEADER_HOME_DIR (toil.leader.AbstractProvisioner attribute) (toil.provisioners.abstractProvisioner.AbstractProvisioner attribute) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner attribute) (toil.provisioners.clusterScaler.AbstractProvisioner attribute) (toil.provisioners.gceProvisioner.AbstractProvisioner attribute) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner attribute) leave() (toil.batchSystems.cleanup_support.LastProcessStandingArena method) (toil.lib.threading.LastProcessStandingArena method) (toil.test.src.threadingTest.LastProcessStandingArena method) leaves() (toil.test.wdl.wdltoil_test.WDLWorkflowGraph method) (toil.wdl.wdltoil.WDLWorkflowGraph method) link_file() (in module toil.server.utils) (in module toil.server.wes.tasks) link_merge() (toil.cwl.cwltoil.ResolveSource method) list_all_file_names() (toil.cwl.cwltoil.FileJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) list_objects_for_url() (in module toil.jobStores.aws.jobStore) (in module toil.lib.aws.utils) list_runs() (toil.server.app.ToilBackend method) (toil.server.wes.abstract_backend.WESBackend method) (toil.server.wes.toil_backend.ToilBackend method) (toil.server.wes.toil_backend.WESBackend method) list_url() (toil.cwl.cwltoil.AbstractJobStore class method) (toil.cwl.utils.AbstractJobStore class method) (toil.fileStores.abstractFileStore.AbstractJobStore class method) (toil.fileStores.cachingFileStore.AbstractJobStore class method) (toil.fileStores.nonCachingFileStore.AbstractJobStore class method) (toil.jobStores.abstractJobStore.AbstractJobStore class method) (toil.jobStores.aws.jobStore.AbstractJobStore class method) (toil.jobStores.fileJobStore.AbstractJobStore class method) (toil.jobStores.googleJobStore.AbstractJobStore class method) (toil.leader.AbstractJobStore class method) (toil.serviceManager.AbstractJobStore class method) (toil.toilState.AbstractJobStore class method) (toil.utils.toilStats.AbstractJobStore class method) (toil.wdl.wdltoil.AbstractJobStore class method) (toil.worker.AbstractJobStore class method) listdir() (toil.cwl.cwltoil.ToilFsAccess method) load() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.deferred.ModuleDescriptor method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.job.ModuleDescriptor method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo class method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.resource.ModuleDescriptor method) (toil.server.wsgi_app.GunicornApplication method) (toil.serviceManager.AbstractJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo class method) (toil.test.src.jobDescriptionTest.ModuleDescriptor method) (toil.test.src.resourceTest.ModuleDescriptor method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) load_config() (toil.server.wsgi_app.GunicornApplication method) load_contents() (toil.test.cwl.cwlTest.CWLWorkflowTest method) load_job() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) load_root_job() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) load_workflow() (toil.leader.ToilState method) (toil.serviceManager.ToilState method) (toil.toilState.ToilState method) loadJob() (toil.cwl.cwltoil.Job class method) (toil.fileStores.abstractFileStore.Job class method) (toil.fileStores.cachingFileStore.Job class method) (toil.fileStores.nonCachingFileStore.Job class method) (toil.job.Job class method) (toil.jobStores.aws.jobStore.Job class method) (toil.test.batchSystems.batchSystemTest.Job class method) (toil.test.jobStores.jobStoreTest.Job class method) (toil.test.lib.dockerTest.Job class method) (toil.test.mesos.helloWorld.Job class method) (toil.test.mesos.stress.Job class method) (toil.test.provisioners.restartScript.Job class method) (toil.test.sort.restart_sort.Job class method) (toil.test.sort.sort.Job class method) (toil.test.sort.sortTest.Job class method) (toil.test.src.busTest.Job class method) (toil.test.src.checkpointTest.Job class method) (toil.test.src.deferredFunctionTest.Job class method) (toil.test.src.environmentTest.Job class method) (toil.test.src.fileStoreTest.Job class method) (toil.test.src.helloWorldTest.Job class method) (toil.test.src.importExportFileTest.Job class method) (toil.test.src.jobDescriptionTest.Job class method) (toil.test.src.jobEncapsulationTest.Job class method) (toil.test.src.jobFileStoreTest.Job class method) (toil.test.src.jobServiceTest.Job class method) (toil.test.src.jobTest.Job class method) (toil.test.src.promisedRequirementTest.Job class method) (toil.test.src.promisesTest.Job class method) (toil.test.src.realtimeLoggerTest.Job class method) (toil.test.src.restartDAGTest.Job class method) (toil.test.src.resumabilityTest.Job class method) (toil.test.src.retainTempDirTest.Job class method) (toil.test.src.toilContextManagerTest.Job class method) (toil.test.src.userDefinedJobArgTypeTest.Job class method) (toil.test.utils.utilsTest.Job class method) (toil.utils.toilStats.Job class method) (toil.wdl.wdltoil.Job class method) (toil.worker.Job class method) loadModules() (in module toil.utils.toilMain) loadOrCreate() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo class method) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo class method) loadOrFail() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo class method) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo class method) loadRootJob() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) localDirPath (toil.batchSystems.abstractBatchSystem.Resource property) (toil.batchSystems.awsBatch.Resource property) (toil.batchSystems.contained_executor.Resource property) (toil.batchSystems.kubernetes.Resource property) (toil.batchSystems.mesos.executor.Resource property) (toil.resource.Resource property) (toil.test.src.resourceTest.Resource property) localize() (toil.deferred.ModuleDescriptor method) (toil.job.ModuleDescriptor method) (toil.resource.ModuleDescriptor method) (toil.test.src.jobDescriptionTest.ModuleDescriptor method) (toil.test.src.resourceTest.ModuleDescriptor method) localPath (toil.batchSystems.abstractBatchSystem.Resource property) (toil.batchSystems.awsBatch.Resource property) (toil.batchSystems.contained_executor.Resource property) (toil.batchSystems.kubernetes.Resource property) (toil.batchSystems.mesos.executor.Resource property) (toil.resource.DirectoryResource property) (toil.resource.FileResource property) (toil.resource.Resource property) (toil.test.src.resourceTest.Resource property) LocalThrottle (class in toil.leader) (class in toil.lib.throttle) (class in toil.serviceManager) locator (toil.cwl.cwltoil.AbstractJobStore property) (toil.cwl.utils.AbstractJobStore property) (toil.fileStores.abstractFileStore.AbstractJobStore property) (toil.fileStores.cachingFileStore.AbstractJobStore property) (toil.fileStores.nonCachingFileStore.AbstractJobStore property) (toil.jobStores.abstractJobStore.AbstractJobStore property) (toil.jobStores.aws.jobStore.AbstractJobStore property) (toil.jobStores.fileJobStore.AbstractJobStore property) (toil.jobStores.googleJobStore.AbstractJobStore property) (toil.leader.AbstractJobStore property) (toil.serviceManager.AbstractJobStore property) (toil.toilState.AbstractJobStore property) (toil.utils.toilStats.AbstractJobStore property) (toil.wdl.wdltoil.AbstractJobStore property) (toil.worker.AbstractJobStore property) LocatorException, [1], [2], [3] lock (toil.batchSystems.mesos.test.MesosTestSupport.MesosThread attribute) (toil.common.RealtimeLogger attribute) (toil.deferred.RealtimeLogger attribute) (toil.realtimeLogger.RealtimeLogger attribute) (toil.test.ApplianceTestSupport.Appliance attribute) (toil.test.batchSystems.batchSystemTest.MesosTestSupport.MesosThread attribute) (toil.test.sort.restart_sort.RealtimeLogger attribute) (toil.test.sort.sort.RealtimeLogger attribute) (toil.test.sort.sortTest.MesosTestSupport.MesosThread attribute) (toil.test.src.autoDeploymentTest.ApplianceTestSupport.Appliance attribute) (toil.test.src.fileStoreTest.RealtimeLogger attribute) (toil.test.src.promisedRequirementTest.MesosTestSupport.MesosThread attribute) (toil.test.src.realtimeLoggerTest.RealtimeLogger attribute) log (in module toil) (in module toil.batchSystems.mesos.batchSystem) (in module toil.batchSystems.mesos.executor) (in module toil.batchSystems.mesos.test) (in module toil.jobStores.googleJobStore) (in module toil.jobStores.utils) (in module toil.test.cwl.cwlTest) (in module toil.test.provisioners.aws.awsProvisionerTest) (in module toil.test.provisioners.clusterTest) (in module toil.test.provisioners.gceProvisionerTest) (in module toil.test.provisioners.provisionerTest) (in module toil.test.src.miscTests) (in module toil.test.src.promisedRequirementTest) (in module toil.test.src.threadingTest) log() (toil.common.ToilMetrics method) (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.Job method) (toil.jobStores.aws.jobStore.Job method) (toil.leader.ToilMetrics method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method)

log_bindings() (in module toil.wdl.wdltoil) log_for_run() (toil.server.wes.abstract_backend.WESBackend static method) (toil.server.wes.toil_backend.WESBackend static method) log_to_file() (in module toil.statsAndLogging) log_to_leader() (toil.batchSystems.abstractBatchSystem.AbstractFileStore method) (toil.cwl.cwltoil.AbstractFileStore method) (toil.cwl.utils.AbstractFileStore method) (toil.fileStores.abstractFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.AbstractFileStore method) (toil.fileStores.nonCachingFileStore.AbstractFileStore method) (toil.test.cwl.cwlTest.AbstractFileStore method) (toil.wdl.wdltoil.AbstractFileStore method) (toil.worker.AbstractFileStore method) log_user_stream() (toil.batchSystems.abstractBatchSystem.AbstractFileStore method) (toil.cwl.cwltoil.AbstractFileStore method) (toil.cwl.utils.AbstractFileStore method) (toil.fileStores.abstractFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.AbstractFileStore method) (toil.fileStores.nonCachingFileStore.AbstractFileStore method) (toil.test.cwl.cwlTest.AbstractFileStore method) (toil.wdl.wdltoil.AbstractFileStore method) (toil.worker.AbstractFileStore method) logAccess() (toil.batchSystems.abstractBatchSystem.AbstractFileStore method) (toil.cwl.cwltoil.AbstractFileStore method) (toil.cwl.utils.AbstractFileStore method) (toil.fileStores.abstractFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.AbstractFileStore method) (toil.fileStores.nonCachingFileStore.AbstractFileStore method) (toil.test.cwl.cwlTest.AbstractFileStore method) (toil.wdl.wdltoil.AbstractFileStore method) (toil.worker.AbstractFileStore method) logClusterDesiredSize() (toil.common.ToilMetrics method) (toil.leader.ToilMetrics method) logClusterSize() (toil.common.ToilMetrics method) (toil.leader.ToilMetrics method) logCompletedJob() (toil.common.ToilMetrics method) (toil.leader.ToilMetrics method) logDiskUsage() (in module toil.test.src.promisedRequirementTest) logFailedJob() (toil.common.ToilMetrics method) (toil.leader.ToilMetrics method) logFile (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) logger (in module toil.batchSystems.abstractBatchSystem) (in module toil.batchSystems.abstractGridEngineBatchSystem) (in module toil.batchSystems.awsBatch) (in module toil.batchSystems.cleanup_support) (in module toil.batchSystems.contained_executor) (in module toil.batchSystems.gridengine) (in module toil.batchSystems.htcondor) (in module toil.batchSystems.kubernetes) (in module toil.batchSystems.local_support) (in module toil.batchSystems.lsf) (in module toil.batchSystems.lsfHelper) (in module toil.batchSystems.options) (in module toil.batchSystems.registry) (in module toil.batchSystems.singleMachine) (in module toil.batchSystems.slurm) (in module toil.batchSystems.torque) (in module toil.bus) (in module toil.common) (in module toil.cwl.cwltoil) (in module toil.cwl.utils) (in module toil.deferred) (in module toil.exceptions) (in module toil.fileStores.abstractFileStore) (in module toil.fileStores.cachingFileStore) (in module toil.fileStores.nonCachingFileStore) (in module toil.job) (in module toil.jobStores.abstractJobStore) (in module toil.jobStores.aws.jobStore) (in module toil.jobStores.aws.utils) (in module toil.jobStores.fileJobStore) (in module toil.leader) (in module toil.lib.aws) (in module toil.lib.aws.ami) (in module toil.lib.aws.iam) (in module toil.lib.aws.session) (in module toil.lib.aws.utils) (in module toil.lib.bioio) (in module toil.lib.docker) (in module toil.lib.ec2) (in module toil.lib.ec2nodes) (in module toil.lib.humanize) (in module toil.lib.io) (in module toil.lib.misc) (in module toil.lib.retry) (in module toil.lib.threading) (in module toil.options.common) (in module toil.provisioners) (in module toil.provisioners.abstractProvisioner) (in module toil.provisioners.aws) (in module toil.provisioners.aws.awsProvisioner) (in module toil.provisioners.clusterScaler) (in module toil.provisioners.gceProvisioner) (in module toil.provisioners.node) (in module toil.realtimeLogger) (in module toil.resource) (in module toil.server.app) (in module toil.server.cli.wes_cwl_runner) (in module toil.server.utils) (in module toil.server.wes.abstract_backend) (in module toil.server.wes.amazon_wes_utils) (in module toil.server.wes.tasks) (in module toil.server.wes.toil_backend) (in module toil.serviceManager) (in module toil.statsAndLogging) (in module toil.test) (in module toil.test.batchSystems.batch_system_plugin_test) (in module toil.test.batchSystems.batchSystemTest) (in module toil.test.jobStores.jobStoreTest) (in module toil.test.lib.aws.test_iam) (in module toil.test.lib.aws.test_s3) (in module toil.test.lib.aws.test_utils) (in module toil.test.lib.dockerTest) (in module toil.test.lib.test_conversions) (in module toil.test.lib.test_ec2) (in module toil.test.lib.test_misc) (in module toil.test.provisioners.clusterScalerTest) (in module toil.test.server.serverTest) (in module toil.test.sort.sortTest) (in module toil.test.src.autoDeploymentTest) (in module toil.test.src.busTest) (in module toil.test.src.deferredFunctionTest) (in module toil.test.src.environmentTest) (in module toil.test.src.fileStoreTest) (in module toil.test.src.jobFileStoreTest) (in module toil.test.src.jobServiceTest) (in module toil.test.src.jobTest) (in module toil.test.src.regularLogTest) (in module toil.test.src.restartDAGTest) (in module toil.test.utils.toilDebugTest) (in module toil.test.utils.toilKillTest) (in module toil.test.utils.utilsTest) (in module toil.toilState) (in module toil.utils.toilClean) (in module toil.utils.toilConfig) (in module toil.utils.toilDebugFile) (in module toil.utils.toilDebugJob) (in module toil.utils.toilDestroyCluster) (in module toil.utils.toilKill) (in module toil.utils.toilLaunchCluster) (in module toil.utils.toilRsyncCluster) (in module toil.utils.toilServer) (in module toil.utils.toilSshCluster) (in module toil.utils.toilStats) (in module toil.utils.toilStatus) (in module toil.utils.toilUpdateEC2Instances) (in module toil.wdl.wdltoil) (in module toil.worker) (toil.common.RealtimeLogger attribute) (toil.deferred.RealtimeLogger attribute) (toil.realtimeLogger.RealtimeLogger attribute) (toil.test.sort.restart_sort.RealtimeLogger attribute) (toil.test.sort.sort.RealtimeLogger attribute) (toil.test.src.fileStoreTest.RealtimeLogger attribute) (toil.test.src.realtimeLoggerTest.RealtimeLogger attribute) LoggingDatagramHandler (class in toil.realtimeLogger) loggingServer (toil.common.RealtimeLogger attribute) (toil.deferred.RealtimeLogger attribute) (toil.realtimeLogger.RealtimeLogger attribute) (toil.test.sort.restart_sort.RealtimeLogger attribute) (toil.test.sort.sort.RealtimeLogger attribute) (toil.test.src.fileStoreTest.RealtimeLogger attribute) (toil.test.src.realtimeLoggerTest.RealtimeLogger attribute) logIssuedJob() (toil.common.ToilMetrics method) (toil.leader.ToilMetrics method) logLevel (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) logMissingJob() (toil.common.ToilMetrics method) (toil.leader.ToilMetrics method) logProcessContext() (in module toil) (in module toil.common) (in module toil.worker) logQueueSize() (toil.common.ToilMetrics method) (toil.leader.ToilMetrics method) logRotating (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) LogTest (class in toil.test.src.realtimeLoggerTest) logToMaster() (toil.batchSystems.abstractBatchSystem.AbstractFileStore method) (toil.cwl.cwltoil.AbstractFileStore method) (toil.cwl.utils.AbstractFileStore method) (toil.fileStores.abstractFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.AbstractFileStore method) (toil.fileStores.nonCachingFileStore.AbstractFileStore method) (toil.test.cwl.cwlTest.AbstractFileStore method) (toil.wdl.wdltoil.AbstractFileStore method) (toil.worker.AbstractFileStore method) logWithFormatting() (toil.exceptions.StatsAndLogging class method) (toil.leader.StatsAndLogging class method) (toil.statsAndLogging.StatsAndLogging class method) (toil.test.jobStores.jobStoreTest.StatsAndLogging class method) (toil.utils.toilStatus.StatsAndLogging class method) LONG_FORMS (in module toil.utils.toilStats) LongTestFollowOn (class in toil.test.mesos.stress) LongTestJob (class in toil.test.mesos.stress) lookup() (toil.batchSystems.abstractBatchSystem.Resource class method) (toil.batchSystems.awsBatch.Resource class method) (toil.batchSystems.contained_executor.Resource class method) (toil.batchSystems.kubernetes.Resource class method) (toil.batchSystems.mesos.executor.Resource class method) (toil.resource.Resource class method) (toil.test.src.resourceTest.Resource class method) lookupEnvVar() (in module toil) (in module toil.common) LOST (toil.batchSystems.abstractBatchSystem.BatchJobExitReason attribute) (toil.batchSystems.abstractGridEngineBatchSystem.BatchJobExitReason attribute) (toil.batchSystems.awsBatch.BatchJobExitReason attribute) (toil.batchSystems.kubernetes.BatchJobExitReason attribute) (toil.batchSystems.lsf.BatchJobExitReason attribute) (toil.batchSystems.mesos.batchSystem.BatchJobExitReason attribute) (toil.batchSystems.slurm.BatchJobExitReason attribute) (toil.leader.BatchJobExitReason attribute) (toil.test.batchSystems.test_slurm.BatchJobExitReason attribute) (toil.test.src.busTest.BatchJobExitReason attribute) LSB_PARAMS_FILENAME (in module toil.batchSystems.lsfHelper) lsf_batch_system_factory() (in module toil.batchSystems.registry) LSF_CONF_ENV (in module toil.batchSystems.lsfHelper) LSF_CONF_FILENAME (in module toil.batchSystems.lsfHelper) LSF_JSON_OUTPUT_MIN_VERSION (in module toil.batchSystems.lsfHelper) LSFBatchSystem (class in toil.batchSystems.lsf) LSFBatchSystem.GridEngineThread (class in toil.batchSystems.lsf) LSFBatchSystemTest (class in toil.test.batchSystems.batchSystemTest) LSFHelperTest (class in toil.test.batchSystems.test_lsf_helper)

M

MagicExpando (class in toil.lib.expando) (class in toil.worker) main() (in module toil.batchSystems.mesos.executor) (in module toil.cwl.cwltoil) (in module toil.server.cli.wes_cwl_runner) (in module toil.test.mesos.helloWorld) (in module toil.test.mesos.stress) (in module toil.test.sort.restart_sort) (in module toil.test.sort.sort) (in module toil.test.sort.sortTest) (in module toil.test.src.environmentTest) (in module toil.test.src.userDefinedJobArgTypeTest) (in module toil.utils.toilClean) (in module toil.utils.toilConfig) (in module toil.utils.toilDebugFile) (in module toil.utils.toilDebugJob) (in module toil.utils.toilDestroyCluster) (in module toil.utils.toilKill) (in module toil.utils.toilLaunchCluster) (in module toil.utils.toilMain) (in module toil.utils.toilRsyncCluster) (in module toil.utils.toilServer) (in module toil.utils.toilSshCluster) (in module toil.utils.toilStats) (in module toil.utils.toilStatus) (in module toil.utils.toilUpdateEC2Instances) (in module toil.wdl.wdltoil) (in module toil.worker) mainCacheTag (in module toil.version) make_gather_bindings() (toil.test.wdl.wdltoil_test.WDLSectionJob method) (toil.wdl.wdltoil.WDLSectionJob method) make_open_interval_action() (in module toil.batchSystems.singleMachine) (in module toil.options.common) make_path_mapper() (toil.cwl.cwltoil.ToilTool method) make_public_dir() (in module toil.fileStores.cachingFileStore) (in module toil.fileStores.nonCachingFileStore) (in module toil.lib.io) (in module toil.worker) make_tests() (in module toil.test) (in module toil.test.jobStores.jobStoreTest) makeFileToSort() (in module toil.test.sort.restart_sort) (in module toil.test.sort.sort) (in module toil.test.sort.sortTest) (in module toil.test.utils.utilsTest) makeImportExportTests() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test class method) makeJob() (in module toil.cwl.cwltoil) makeJobGraph() (toil.test.src.jobTest.JobTest method) makeLoadable() (toil.deferred.ModuleDescriptor method) (toil.job.ModuleDescriptor method) (toil.resource.ModuleDescriptor method) (toil.test.src.jobDescriptionTest.ModuleDescriptor method) (toil.test.src.resourceTest.ModuleDescriptor method) makePickle() (toil.realtimeLogger.JSONDatagramHandler method) makeRandomDAG() (toil.test.src.jobTest.JobTest static method) MalformedRequestException ManagedNodesNotSupportedException, [1] manager (in module toil.lib.ec2nodes) manualMemArgs (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) map_over_files_in_bindings() (in module toil.wdl.wdltoil) map_over_typed_files_in_binding() (in module toil.wdl.wdltoil) map_over_typed_files_in_bindings() (in module toil.wdl.wdltoil) map_over_typed_files_in_value() (in module toil.wdl.wdltoil) MAT (in module toil.lib.memoize) MAX_BATCH_SIZE (in module toil.jobStores.googleJobStore) MAX_CANCELING_SECONDS (in module toil.server.utils) max_jobs (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) max_local_jobs (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) MAX_POLL_COUNT (in module toil.batchSystems.awsBatch) maxAttributesPerItem (toil.jobStores.aws.jobStore.SDBHelper attribute) (toil.jobStores.aws.utils.SDBHelper attribute) maxBinarySize() (toil.jobStores.aws.jobStore.SDBHelper class method) (toil.jobStores.aws.utils.SDBHelper class method) maxBucketNameLen (toil.jobStores.aws.jobStore.AWSJobStore attribute) (toil.test.lib.aws.test_s3.AWSJobStore attribute) maxConcurrency() (in module toil.test.src.promisedRequirementTest) maxCores (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) MaxCoresSingleMachineBatchSystemTest (class in toil.test.batchSystems.batchSystemTest) maxDisk (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) maxInlinedSize() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo static method) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo static method) MAXJOBDURATION (toil.batchSystems.abstractBatchSystem.BatchJobExitReason attribute) maxJobDuration (toil.batchSystems.abstractBatchSystem.Config attribute) MAXJOBDURATION (toil.batchSystems.abstractGridEngineBatchSystem.BatchJobExitReason attribute) (toil.batchSystems.awsBatch.BatchJobExitReason attribute) maxJobDuration (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) MAXJOBDURATION (toil.batchSystems.kubernetes.BatchJobExitReason attribute) maxJobDuration (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) MAXJOBDURATION (toil.batchSystems.lsf.BatchJobExitReason attribute) (toil.batchSystems.mesos.batchSystem.BatchJobExitReason attribute) maxJobDuration (toil.batchSystems.singleMachine.Config attribute) MAXJOBDURATION (toil.batchSystems.slurm.BatchJobExitReason attribute) maxJobDuration (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) MAXJOBDURATION (toil.leader.BatchJobExitReason attribute) maxJobDuration (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) MAXJOBDURATION (toil.test.batchSystems.test_slurm.BatchJobExitReason attribute) maxJobDuration (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) MAXJOBDURATION (toil.test.src.busTest.BatchJobExitReason attribute) maxJobDuration (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) maxLogFileSize (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) maxMemory (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) maxNameLen (toil.jobStores.aws.jobStore.AWSJobStore attribute) (toil.test.lib.aws.test_s3.AWSJobStore attribute) maxNodes (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) maxPreemptibleServiceJobs (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) maxRawValueSize (toil.jobStores.aws.jobStore.SDBHelper attribute) (toil.jobStores.aws.utils.SDBHelper attribute) maxServiceJobs (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) maxValueSize (toil.jobStores.aws.jobStore.SDBHelper attribute) (toil.jobStores.aws.utils.SDBHelper attribute) maxWaitTime (toil.provisioners.abstractProvisioner.Node attribute) (toil.provisioners.aws.awsProvisioner.Node attribute) (toil.provisioners.gceProvisioner.Node attribute) (toil.provisioners.node.Node attribute) (toil.test.provisioners.clusterScalerTest.Node attribute) measureConcurrency() (in module toil.test.batchSystems.batchSystemTest) meets_boto_error_code_condition() (in module toil.lib.retry) meets_error_code_condition() (in module toil.lib.retry) meets_error_message_condition() (in module toil.lib.retry) MEMLIMIT (toil.batchSystems.abstractBatchSystem.BatchJobExitReason attribute) (toil.batchSystems.abstractGridEngineBatchSystem.BatchJobExitReason attribute) (toil.batchSystems.awsBatch.BatchJobExitReason attribute) (toil.batchSystems.kubernetes.BatchJobExitReason attribute) (toil.batchSystems.lsf.BatchJobExitReason attribute) (toil.batchSystems.mesos.batchSystem.BatchJobExitReason attribute) (toil.batchSystems.slurm.BatchJobExitReason attribute) (toil.leader.BatchJobExitReason attribute) (toil.test.batchSystems.test_slurm.BatchJobExitReason attribute) (toil.test.src.busTest.BatchJobExitReason attribute) memoize (in module toil) (in module toil.batchSystems.abstractBatchSystem) (in module toil.batchSystems.registry) (in module toil.jobStores.abstractJobStore) (in module toil.lib.accelerators) (in module toil.lib.memoize) (in module toil.provisioners.aws.awsProvisioner) (in module toil.test) (in module toil.test.jobStores.jobStoreTest) (in module toil.wdl.wdltoil) memory (toil.batchSystems.abstractBatchSystem.Requirer property) (toil.batchSystems.awsBatch.Requirer property) (toil.batchSystems.kubernetes.Requirer property) (toil.batchSystems.singleMachine.Requirer property) (toil.batchSystems.slurm.Requirer property) (toil.cwl.cwltoil.Job property) (toil.fileStores.abstractFileStore.Job property) (toil.fileStores.cachingFileStore.Job property) (toil.fileStores.nonCachingFileStore.Job property) (toil.job.Job property) (toil.job.RequirementsDict attribute) (toil.job.Requirer property) (toil.jobStores.aws.jobStore.Job property) (toil.test.batchSystems.batchSystemTest.Job property) (toil.test.batchSystems.batchSystemTest.Requirer property) (toil.test.jobStores.jobStoreTest.Job property) (toil.test.lib.dockerTest.Job property) (toil.test.mesos.helloWorld.Job property) (toil.test.mesos.stress.Job property) (toil.test.provisioners.restartScript.Job property) (toil.test.sort.restart_sort.Job property) (toil.test.sort.sort.Job property) (toil.test.sort.sortTest.Job property) (toil.test.src.busTest.Job property) (toil.test.src.checkpointTest.Job property) (toil.test.src.deferredFunctionTest.Job property) (toil.test.src.environmentTest.Job property) (toil.test.src.fileStoreTest.Job property) (toil.test.src.helloWorldTest.Job property) (toil.test.src.importExportFileTest.Job property) (toil.test.src.jobDescriptionTest.Job property) (toil.test.src.jobEncapsulationTest.Job property) (toil.test.src.jobFileStoreTest.Job property) (toil.test.src.jobServiceTest.Job property) (toil.test.src.jobTest.Job property) (toil.test.src.promisedRequirementTest.Job property) (toil.test.src.promisesTest.Job property) (toil.test.src.realtimeLoggerTest.Job property) (toil.test.src.restartDAGTest.Job property) (toil.test.src.resumabilityTest.Job property) (toil.test.src.retainTempDirTest.Job property) (toil.test.src.toilContextManagerTest.Job property) (toil.test.src.userDefinedJobArgTypeTest.Job property) (toil.test.utils.utilsTest.Job property) (toil.utils.toilStats.Job property) (toil.wdl.wdltoil.Job property) (toil.worker.Job property) MemoryStateCache (class in toil.server.utils) MemoryStateStore (class in toil.server.utils) merge() (in module toil.test.sort.restart_sort) (in module toil.test.sort.sort) (in module toil.test.sort.sortTest) mesos_batch_system_factory() (in module toil.batchSystems.registry) mesos_endpoint (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) mesos_framework_id (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute)

mesos_name (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) mesos_role (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) MesosBatchSystem (class in toil.batchSystems.mesos.batchSystem) MesosBatchSystem.ExecutorInfo (class in toil.batchSystems.mesos.batchSystem) MesosBatchSystemJobTest (class in toil.test.batchSystems.batchSystemTest) MesosBatchSystemTest (class in toil.test.batchSystems.batchSystemTest) mesosCommand() (toil.batchSystems.mesos.test.MesosTestSupport.MesosAgentThread method) (toil.batchSystems.mesos.test.MesosTestSupport.MesosMasterThread method) (toil.batchSystems.mesos.test.MesosTestSupport.MesosThread method) (toil.test.batchSystems.batchSystemTest.MesosTestSupport.MesosAgentThread method) (toil.test.batchSystems.batchSystemTest.MesosTestSupport.MesosMasterThread method) (toil.test.batchSystems.batchSystemTest.MesosTestSupport.MesosThread method) (toil.test.sort.sortTest.MesosTestSupport.MesosAgentThread method) (toil.test.sort.sortTest.MesosTestSupport.MesosMasterThread method) (toil.test.sort.sortTest.MesosTestSupport.MesosThread method) (toil.test.src.promisedRequirementTest.MesosTestSupport.MesosAgentThread method) (toil.test.src.promisedRequirementTest.MesosTestSupport.MesosMasterThread method) (toil.test.src.promisedRequirementTest.MesosTestSupport.MesosThread method) MesosExecutor (class in toil.batchSystems.mesos.executor) MesosPromisedRequirementsTest (class in toil.test.src.promisedRequirementTest) MesosShape (class in toil.batchSystems.mesos) (class in toil.batchSystems.mesos.batchSystem) MesosTestSupport (class in toil.batchSystems.mesos.test) (class in toil.test.batchSystems.batchSystemTest) (class in toil.test.sort.sortTest) (class in toil.test.src.promisedRequirementTest) MesosTestSupport.MesosAgentThread (class in toil.batchSystems.mesos.test) (class in toil.test.batchSystems.batchSystemTest) (class in toil.test.sort.sortTest) (class in toil.test.src.promisedRequirementTest) MesosTestSupport.MesosMasterThread (class in toil.batchSystems.mesos.test) (class in toil.test.batchSystems.batchSystemTest) (class in toil.test.sort.sortTest) (class in toil.test.src.promisedRequirementTest) MesosTestSupport.MesosThread (class in toil.batchSystems.mesos.test) (class in toil.test.batchSystems.batchSystemTest) (class in toil.test.sort.sortTest) (class in toil.test.src.promisedRequirementTest) message (toil.fileStores.cachingFileStore.CacheUnbalancedError attribute) (toil.test.src.fileStoreTest.CacheUnbalancedError attribute) message_to_bytes() (in module toil.bus) MessageBus (class in toil.batchSystems.abstractBatchSystem) (class in toil.bus) (class in toil.common) (class in toil.test.src.busTest) (class in toil.toilState) MessageBusClient (class in toil.bus) MessageBusConnection (class in toil.bus) MessageBusTest (class in toil.test.src.busTest) MessageDetector (class in toil.test.src.realtimeLoggerTest) MessageInbox (class in toil.bus) MessageOutbox (class in toil.batchSystems.abstractBatchSystem) (class in toil.bus) MessageType (in module toil.bus) (toil.batchSystems.abstractBatchSystem.MessageBus attribute) (toil.bus.MessageBus attribute) (toil.bus.MessageInbox attribute) (toil.common.MessageBus attribute) (toil.test.src.busTest.MessageBus attribute) (toil.toilState.MessageBus attribute) methodNamePartRegex (in module toil.test) metrics (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) mib_to_b() (in module toil.batchSystems.mesos.batchSystem) (in module toil.lib.conversions) MIN_REQUESTABLE_CORES (in module toil.batchSystems.awsBatch) MIN_REQUESTABLE_MIB (in module toil.batchSystems.awsBatch) minBucketNameLen (toil.jobStores.aws.jobStore.AWSJobStore attribute) (toil.test.lib.aws.test_s3.AWSJobStore attribute) minCores (toil.batchSystems.local_support.SingleMachineBatchSystem attribute) (toil.batchSystems.singleMachine.SingleMachineBatchSystem attribute) (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystem attribute) (toil.test.src.jobServiceTest.SingleMachineBatchSystem attribute) minNodes (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) MiscTests (class in toil.test.src.miscTests) MISSING (toil.batchSystems.abstractBatchSystem.BatchJobExitReason attribute) (toil.batchSystems.abstractGridEngineBatchSystem.BatchJobExitReason attribute) (toil.batchSystems.awsBatch.BatchJobExitReason attribute) (toil.batchSystems.kubernetes.BatchJobExitReason attribute) (toil.batchSystems.lsf.BatchJobExitReason attribute) (toil.batchSystems.mesos.batchSystem.BatchJobExitReason attribute) (toil.batchSystems.slurm.BatchJobExitReason attribute) (toil.leader.BatchJobExitReason attribute) (toil.test.batchSystems.test_slurm.BatchJobExitReason attribute) (toil.test.src.busTest.BatchJobExitReason attribute) MISSING_FILE (in module toil.cwl.cwltoil) mkdtemp() (in module toil.cwl.cwltoil) (in module toil.fileStores.abstractFileStore) (in module toil.fileStores.cachingFileStore) (in module toil.jobStores.fileJobStore) (in module toil.lib.io) (in module toil.resource) (in module toil.server.wes.abstract_backend) (in module toil.test) (in module toil.test.jobStores.jobStoreTest) (in module toil.test.src.miscTests) (in module toil.test.src.systemTest) (in module toil.wdl.wdltoil) MockBatchSystemAndProvisioner (class in toil.test.provisioners.clusterScalerTest) model (toil.batchSystems.abstractGridEngineBatchSystem.AcceleratorRequirement attribute) (toil.batchSystems.htcondor.AcceleratorRequirement attribute) (toil.batchSystems.singleMachine.AcceleratorRequirement attribute) (toil.cwl.cwltoil.AcceleratorRequirement attribute) (toil.job.AcceleratorRequirement attribute) (toil.lib.accelerators.AcceleratorRequirement attribute) (toil.wdl.wdltoil.AcceleratorRequirement attribute) modify_param_paths() (toil.server.cli.wes_cwl_runner.WESClientWithWorkflowEngineParameters method) module toil toil.batchSystems toil.batchSystems.abstractBatchSystem toil.batchSystems.abstractGridEngineBatchSystem toil.batchSystems.awsBatch toil.batchSystems.cleanup_support toil.batchSystems.contained_executor toil.batchSystems.gridengine toil.batchSystems.htcondor toil.batchSystems.kubernetes toil.batchSystems.local_support toil.batchSystems.lsf toil.batchSystems.lsfHelper toil.batchSystems.mesos toil.batchSystems.mesos.batchSystem toil.batchSystems.mesos.conftest toil.batchSystems.mesos.executor toil.batchSystems.mesos.test toil.batchSystems.options toil.batchSystems.registry toil.batchSystems.singleMachine toil.batchSystems.slurm toil.batchSystems.torque toil.bus toil.common toil.cwl toil.cwl.conftest toil.cwl.cwltoil toil.cwl.utils toil.deferred toil.exceptions toil.fileStores toil.fileStores.abstractFileStore toil.fileStores.cachingFileStore toil.fileStores.nonCachingFileStore toil.job toil.jobStores toil.jobStores.abstractJobStore toil.jobStores.aws toil.jobStores.aws.jobStore toil.jobStores.aws.utils toil.jobStores.conftest toil.jobStores.fileJobStore toil.jobStores.googleJobStore toil.jobStores.utils toil.leader toil.lib toil.lib.accelerators toil.lib.aws toil.lib.aws.ami toil.lib.aws.iam toil.lib.aws.session toil.lib.aws.utils toil.lib.bioio toil.lib.compatibility toil.lib.conversions toil.lib.docker toil.lib.ec2 toil.lib.ec2nodes toil.lib.encryption toil.lib.encryption.conftest toil.lib.exceptions toil.lib.expando toil.lib.generatedEC2Lists toil.lib.humanize toil.lib.io toil.lib.iterables toil.lib.memoize toil.lib.misc toil.lib.objects toil.lib.resources toil.lib.retry toil.lib.threading toil.lib.throttle toil.options toil.options.common toil.options.cwl toil.options.wdl toil.provisioners toil.provisioners.abstractProvisioner toil.provisioners.aws toil.provisioners.aws.awsProvisioner toil.provisioners.clusterScaler toil.provisioners.gceProvisioner toil.provisioners.node toil.realtimeLogger toil.resource toil.server toil.server.api_spec toil.server.app toil.server.celery_app toil.server.cli toil.server.cli.wes_cwl_runner toil.server.utils toil.server.wes toil.server.wes.abstract_backend toil.server.wes.amazon_wes_utils toil.server.wes.tasks toil.server.wes.toil_backend toil.server.wsgi_app toil.serviceManager toil.statsAndLogging toil.test toil.test.batchSystems toil.test.batchSystems.batch_system_plugin_test toil.test.batchSystems.batchSystemTest toil.test.batchSystems.test_lsf_helper toil.test.batchSystems.test_slurm toil.test.cactus toil.test.cactus.test_cactus_integration toil.test.cwl toil.test.cwl.conftest toil.test.cwl.cwlTest toil.test.docs toil.test.docs.scriptsTest toil.test.jobStores toil.test.jobStores.jobStoreTest toil.test.lib toil.test.lib.aws toil.test.lib.aws.test_iam toil.test.lib.aws.test_s3 toil.test.lib.aws.test_utils toil.test.lib.dockerTest toil.test.lib.test_conversions toil.test.lib.test_ec2 toil.test.lib.test_misc toil.test.mesos toil.test.mesos.helloWorld toil.test.mesos.MesosDataStructuresTest toil.test.mesos.stress toil.test.options toil.test.options.options toil.test.provisioners toil.test.provisioners.aws toil.test.provisioners.aws.awsProvisionerTest toil.test.provisioners.clusterScalerTest toil.test.provisioners.clusterTest toil.test.provisioners.gceProvisionerTest toil.test.provisioners.provisionerTest toil.test.provisioners.restartScript toil.test.server toil.test.server.serverTest toil.test.sort toil.test.sort.restart_sort toil.test.sort.sort toil.test.sort.sortTest toil.test.src toil.test.src.autoDeploymentTest toil.test.src.busTest toil.test.src.checkpointTest toil.test.src.deferredFunctionTest toil.test.src.dockerCheckTest toil.test.src.environmentTest toil.test.src.fileStoreTest toil.test.src.helloWorldTest toil.test.src.importExportFileTest toil.test.src.jobDescriptionTest toil.test.src.jobEncapsulationTest toil.test.src.jobFileStoreTest toil.test.src.jobServiceTest toil.test.src.jobTest toil.test.src.miscTests toil.test.src.promisedRequirementTest toil.test.src.promisesTest toil.test.src.realtimeLoggerTest toil.test.src.regularLogTest toil.test.src.resourceTest toil.test.src.restartDAGTest toil.test.src.resumabilityTest toil.test.src.retainTempDirTest toil.test.src.systemTest toil.test.src.threadingTest toil.test.src.toilContextManagerTest toil.test.src.userDefinedJobArgTypeTest toil.test.src.workerTest toil.test.utils toil.test.utils.toilDebugTest toil.test.utils.toilKillTest toil.test.utils.utilsTest toil.test.wdl toil.test.wdl.wdltoil_test toil.test.wdl.wdltoil_test_kubernetes toil.toilState toil.utils toil.utils.toilClean toil.utils.toilConfig toil.utils.toilDebugFile toil.utils.toilDebugJob toil.utils.toilDestroyCluster toil.utils.toilKill toil.utils.toilLaunchCluster toil.utils.toilMain toil.utils.toilRsyncCluster toil.utils.toilServer toil.utils.toilSshCluster toil.utils.toilStats toil.utils.toilStatus toil.utils.toilUpdateEC2Instances toil.version toil.wdl toil.wdl.utils toil.wdl.wdltoil toil.worker module_string (toil.job.JobBodyReference attribute) ModuleDescriptor (class in toil.deferred) (class in toil.job) (class in toil.resource) (class in toil.test.src.jobDescriptionTest) (class in toil.test.src.resourceTest) monkeypatch_coerce() (in module toil.wdl.wdltoil) monkeyPatchSdbConnection() (in module toil.jobStores.aws.utils) moveOutputs (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) mpTestPartSize (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test attribute) MRT (in module toil.lib.memoize) MT (in module toil.test) MultiprocessingTaskRunner (class in toil.server.wes.tasks) (class in toil.server.wes.toil_backend)

N

name (toil.bus.JobStatus attribute) (toil.deferred.ModuleDescriptor attribute) (toil.job.ModuleDescriptor attribute) (toil.resource.ModuleDescriptor attribute) (toil.server.wes.amazon_wes_utils.JobStatus attribute) (toil.server.wes.toil_backend.JobStatus attribute) (toil.test.src.jobDescriptionTest.ModuleDescriptor attribute) (toil.test.src.resourceTest.ModuleDescriptor attribute) Names (class in toil.bus) (class in toil.job) nameSeparator (toil.jobStores.aws.jobStore.AWSJobStore attribute) (toil.test.lib.aws.test_s3.AWSJobStore attribute) needs_aws_batch() (in module toil.test) (in module toil.test.batchSystems.batchSystemTest) needs_aws_ec2() (in module toil.test) (in module toil.test.cwl.cwlTest) (in module toil.test.lib.test_ec2) (in module toil.test.provisioners.aws.awsProvisionerTest) (in module toil.test.provisioners.clusterTest) (in module toil.test.sort.sortTest) (in module toil.test.src.fileStoreTest) (in module toil.test.utils.utilsTest) needs_aws_s3() (in module toil.test) (in module toil.test.batchSystems.batchSystemTest) (in module toil.test.cwl.cwlTest) (in module toil.test.jobStores.jobStoreTest) (in module toil.test.lib.aws.test_s3) (in module toil.test.server.serverTest) (in module toil.test.utils.toilKillTest) needs_celery_broker() (in module toil.test) (in module toil.test.server.serverTest) needs_cwl() (in module toil.test) (in module toil.test.cwl.cwlTest) (in module toil.test.docs.scriptsTest) (in module toil.test.utils.toilKillTest) (in module toil.test.utils.utilsTest) needs_docker() (in module toil.test) (in module toil.test.cwl.cwlTest) (in module toil.test.docs.scriptsTest) (in module toil.test.lib.dockerTest) (in module toil.test.src.dockerCheckTest) (in module toil.test.utils.utilsTest) needs_docker_cuda() (in module toil.test) (in module toil.test.cwl.cwlTest) (in module toil.test.wdl.wdltoil_test) needs_encryption() (in module toil.test) (in module toil.test.jobStores.jobStoreTest) needs_env_var() (in module toil.test) (in module toil.test.cwl.cwlTest) (in module toil.test.provisioners.clusterTest) needs_fetchable_appliance() (in module toil.test) (in module toil.test.batchSystems.batchSystemTest) (in module toil.test.cwl.cwlTest) (in module toil.test.provisioners.aws.awsProvisionerTest) (in module toil.test.provisioners.clusterTest) (in module toil.test.provisioners.gceProvisionerTest) needs_google_project() (in module toil.test) (in module toil.test.jobStores.jobStoreTest) (in module toil.test.provisioners.gceProvisionerTest) (in module toil.test.sort.sortTest) (in module toil.test.src.fileStoreTest) needs_google_storage() (in module toil.test) (in module toil.test.jobStores.jobStoreTest) (in module toil.test.provisioners.gceProvisionerTest) (in module toil.test.sort.sortTest) (in module toil.test.src.fileStoreTest) (in module toil.test.wdl.wdltoil_test) needs_gridengine() (in module toil.test) (in module toil.test.batchSystems.batchSystemTest) (in module toil.test.cwl.cwlTest) (in module toil.test.sort.sortTest) needs_htcondor() (in module toil.test) (in module toil.test.batchSystems.batchSystemTest) needs_java() (in module toil.test) needs_kubernetes() (in module toil.test) (in module toil.test.batchSystems.batchSystemTest) (in module toil.test.cwl.cwlTest) needs_kubernetes_installed() (in module toil.test) (in module toil.test.batchSystems.batchSystemTest) needs_local_appliance() (in module toil.test) (in module toil.test.src.autoDeploymentTest) needs_local_cuda() (in module toil.test) (in module toil.test.cwl.cwlTest) needs_lsf() (in module toil.test) (in module toil.test.batchSystems.batchSystemTest) (in module toil.test.cwl.cwlTest) needs_mesos() (in module toil.test) (in module toil.test.batchSystems.batchSystemTest) (in module toil.test.cwl.cwlTest) (in module toil.test.provisioners.aws.awsProvisionerTest) (in module toil.test.sort.sortTest) (in module toil.test.src.autoDeploymentTest) (in module toil.test.src.promisedRequirementTest) needs_online() (in module toil.test) (in module toil.test.cwl.cwlTest) (in module toil.test.lib.test_ec2) needs_rsync3() (in module toil.test) (in module toil.test.utils.utilsTest) needs_server() (in module toil.test) (in module toil.test.server.serverTest) needs_singularity() (in module toil.test) needs_singularity_or_docker() (in module toil.test) (in module toil.test.wdl.wdltoil_test) needs_slurm() (in module toil.test) (in module toil.test.batchSystems.batchSystemTest) (in module toil.test.cwl.cwlTest) needs_torque() (in module toil.test) (in module toil.test.batchSystems.batchSystemTest) (in module toil.test.cwl.cwlTest) (in module toil.test.sort.sortTest) needs_wdl() (in module toil.test) (in module toil.test.utils.toilDebugTest) (in module toil.test.wdl.wdltoil_test) needs_wes_server() (in module toil.test) (in module toil.test.cwl.cwlTest) nested_crossproduct_scatter() (toil.cwl.cwltoil.CWLScatter method) nextChainable() (in module toil.test.src.workerTest) (in module toil.worker) nextJobOfType() (toil.batchSystems.mesos.batchSystem.JobQueue method) (toil.batchSystems.mesos.JobQueue method) nextSuccessors() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) no_such_sdb_domain() (in module toil.jobStores.aws.jobStore) (in module toil.jobStores.aws.utils) NoAvailableJobStoreException Node (class in toil.provisioners.abstractProvisioner) (class in toil.provisioners.aws.awsProvisioner) (class in toil.provisioners.gceProvisioner) (class in toil.provisioners.node) (class in toil.test.provisioners.clusterScalerTest) NODE_BOTO_PATH (toil.provisioners.gceProvisioner.GCEProvisioner attribute) NodeInfo (class in toil.batchSystems.abstractBatchSystem) (class in toil.batchSystems.mesos.batchSystem) (class in toil.provisioners.clusterScaler) (class in toil.test.provisioners.clusterScalerTest) nodeInUse() (toil.batchSystems.abstractBatchSystem.AbstractScalableBatchSystem method) (toil.batchSystems.mesos.batchSystem.AbstractScalableBatchSystem method) (toil.batchSystems.mesos.batchSystem.MesosBatchSystem method) (toil.provisioners.clusterScaler.AbstractScalableBatchSystem method) (toil.test.provisioners.clusterScalerTest.AbstractScalableBatchSystem method) (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method)

NodeReservation (class in toil.provisioners.clusterScaler) (class in toil.test.provisioners.clusterScalerTest) nodeReservations (toil.provisioners.clusterScaler.BinPackedFit attribute) (toil.test.provisioners.clusterScalerTest.BinPackedFit attribute) nodeServiceAccountJson (toil.jobStores.googleJobStore.GoogleJobStore attribute) (toil.provisioners.gceProvisioner.GoogleJobStore attribute) nodeStorage (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) nodeStorageOverrides (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) nodeTypes (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) NonCachingFileStore (class in toil.fileStores.nonCachingFileStore) NonCachingFileStoreTestWithAwsJobStore (class in toil.test.src.fileStoreTest) NonCachingFileStoreTestWithFileJobStore (class in toil.test.src.fileStoreTest) NonCachingFileStoreTestWithGoogleJobStore (class in toil.test.src.fileStoreTest) NonDownloadingSize (class in toil.wdl.wdltoil) NONTERMINAL_STATES (in module toil.batchSystems.slurm) noOp() (in module toil.test.src.jobEncapsulationTest) normalize_uri() (toil.batchSystems.abstractBatchSystem.Toil static method) (toil.batchSystems.awsBatch.Toil static method) (toil.batchSystems.cleanup_support.Toil static method) (toil.batchSystems.kubernetes.Toil static method) (toil.batchSystems.singleMachine.Toil static method) (toil.common.Toil static method) (toil.cwl.cwltoil.Toil static method) (toil.fileStores.abstractFileStore.Toil static method) (toil.job.Toil static method) (toil.server.wes.tasks.Toil static method) (toil.test.batchSystems.batch_system_plugin_test.Toil static method) (toil.test.batchSystems.batchSystemTest.Toil static method) (toil.test.jobStores.jobStoreTest.Toil static method) (toil.test.lib.dockerTest.Toil static method) (toil.test.mesos.helloWorld.Toil static method) (toil.test.options.options.Toil static method) (toil.test.sort.restart_sort.Toil static method) (toil.test.sort.sort.Toil static method) (toil.test.sort.sortTest.Toil static method) (toil.test.src.busTest.Toil static method) (toil.test.src.environmentTest.Toil static method) (toil.test.src.fileStoreTest.Toil static method) (toil.test.src.importExportFileTest.Toil static method) (toil.test.src.jobDescriptionTest.Toil static method) (toil.test.src.jobFileStoreTest.Toil static method) (toil.test.src.jobTest.Toil static method) (toil.test.src.restartDAGTest.Toil static method) (toil.test.src.toilContextManagerTest.Toil static method) (toil.test.utils.toilKillTest.Toil static method) (toil.test.utils.utilsTest.Toil static method) (toil.utils.toilClean.Toil static method) (toil.utils.toilDebugFile.Toil static method) (toil.utils.toilDebugJob.Toil static method) (toil.utils.toilKill.Toil static method) (toil.utils.toilStats.Toil static method) (toil.utils.toilStatus.Toil static method) (toil.wdl.wdltoil.Toil static method) (toil.worker.Toil static method) noStdOutErr (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) NoSuchClusterException, [1], [2], [3], [4] NoSuchFileException, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] NoSuchJobException, [1], [2], [3], [4], [5], [6] NoSuchJobStoreException, [1], [2], [3], [4], [5], [6], [7], [8], [9] NoSuchZoneException, [1] not_found() (in module toil.lib.ec2) NOTICE (in module toil.server.wes.amazon_wes_utils) numCores (in module toil.test.batchSystems.batchSystemTest) (toil.batchSystems.local_support.SingleMachineBatchSystem attribute) (toil.batchSystems.singleMachine.SingleMachineBatchSystem attribute) (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystem attribute) (toil.test.src.jobServiceTest.SingleMachineBatchSystem attribute)

O

old_retry() (in module toil.batchSystems.abstractGridEngineBatchSystem) (in module toil.jobStores.aws.utils) (in module toil.jobStores.googleJobStore) (in module toil.lib.aws.utils) (in module toil.lib.ec2) (in module toil.lib.retry) (in module toil.provisioners.aws.awsProvisioner) (in module toil.provisioners.clusterScaler) onRegistration() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.job.ServiceJobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.abstractJobStore.ServiceJobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.leader.ServiceJobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.provisioners.clusterScaler.ServiceJobDescription method) (toil.serviceManager.ServiceJobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.utils.toilStatus.ServiceJobDescription method) (toil.worker.JobDescription method) onWrite() (toil.fileStores.abstractFileStore.WriteWatchingStream method) (toil.jobStores.abstractJobStore.WriteWatchingStream method) (toil.lib.io.WriteWatchingStream method) open() (toil.batchSystems.abstractBatchSystem.AbstractFileStore method) (toil.batchSystems.abstractBatchSystem.DeferredFunctionManager method) (toil.cwl.cwltoil.AbstractFileStore method) (toil.cwl.cwltoil.ToilFsAccess method) (toil.cwl.utils.AbstractFileStore method) (toil.deferred.DeferredFunctionManager method) (toil.fileStores.abstractFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.CachingFileStore method) (toil.fileStores.nonCachingFileStore.AbstractFileStore method) (toil.fileStores.nonCachingFileStore.NonCachingFileStore method) (toil.test.cwl.cwlTest.AbstractFileStore method) (toil.wdl.wdltoil.AbstractFileStore method) (toil.worker.AbstractFileStore method) (toil.worker.DeferredFunctionManager method)

open_url() (toil.cwl.cwltoil.AbstractJobStore class method) (toil.cwl.utils.AbstractJobStore class method) (toil.fileStores.abstractFileStore.AbstractJobStore class method) (toil.fileStores.cachingFileStore.AbstractJobStore class method) (toil.fileStores.nonCachingFileStore.AbstractJobStore class method) (toil.jobStores.abstractJobStore.AbstractJobStore class method) (toil.jobStores.aws.jobStore.AbstractJobStore class method) (toil.jobStores.fileJobStore.AbstractJobStore class method) (toil.jobStores.googleJobStore.AbstractJobStore class method) (toil.leader.AbstractJobStore class method) (toil.serviceManager.AbstractJobStore class method) (toil.toilState.AbstractJobStore class method) (toil.utils.toilStats.AbstractJobStore class method) (toil.wdl.wdltoil.AbstractJobStore class method) (toil.worker.AbstractJobStore class method) OperationForbidden, [1] opt_strtobool() (in module toil.batchSystems.kubernetes) (in module toil.lib.conversions) (in module toil.options.common) (in module toil.utils.toilLaunchCluster) optimize_spot_bid() (in module toil.provisioners.aws) optional_hard_copy() (toil.cwl.cwltoil.FileJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) OptionSetter (class in toil.batchSystems.abstractBatchSystem) (class in toil.batchSystems.awsBatch) (class in toil.batchSystems.kubernetes) (class in toil.batchSystems.mesos.batchSystem) (class in toil.batchSystems.options) (class in toil.batchSystems.singleMachine) (class in toil.batchSystems.slurm) (class in toil.test.batchSystems.batch_system_plugin_test) OptionsTest (class in toil.test.options.options) OptionType (toil.batchSystems.abstractBatchSystem.OptionSetter attribute) (toil.batchSystems.awsBatch.OptionSetter attribute) (toil.batchSystems.kubernetes.KubernetesBatchSystem attribute) (toil.batchSystems.kubernetes.OptionSetter attribute) (toil.batchSystems.mesos.batchSystem.OptionSetter attribute) (toil.batchSystems.options.OptionSetter attribute) (toil.batchSystems.singleMachine.OptionSetter attribute) (toil.batchSystems.slurm.OptionSetter attribute) (toil.batchSystems.slurm.SlurmBatchSystem attribute) (toil.test.batchSystems.batch_system_plugin_test.OptionSetter attribute) OS_SIZE (in module toil.provisioners.clusterScaler) outbox() (toil.batchSystems.abstractBatchSystem.MessageBus method) (toil.bus.MessageBus method) (toil.common.MessageBus method) (toil.test.src.busTest.MessageBus method) (toil.toilState.MessageBus method) outer (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo attribute) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo attribute) ownerID (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo property) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo property)

P

P (toil.batchSystems.kubernetes.KubernetesBatchSystem attribute) (toil.batchSystems.kubernetes.KubernetesBatchSystem.DecoratorWrapper attribute) pack() (toil.common.FileID method) (toil.cwl.cwltoil.FileID method) (toil.cwl.utils.FileID method) (toil.fileStores.abstractFileStore.FileID method) (toil.fileStores.cachingFileStore.FileID method) (toil.fileStores.FileID method) (toil.fileStores.nonCachingFileStore.FileID method) (toil.job.FileID method) (toil.jobStores.abstractJobStore.FileID method) (toil.jobStores.aws.jobStore.FileID method) (toil.jobStores.fileJobStore.FileID method) (toil.test.cwl.cwlTest.FileID method) (toil.test.jobStores.jobStoreTest.FileID method) (toil.test.src.fileStoreTest.FileID method) (toil.test.src.importExportFileTest.FileID method) (toil.test.src.jobFileStoreTest.FileID method) (toil.wdl.wdltoil.FileID method) pack_job() (in module toil.batchSystems.awsBatch) (in module toil.batchSystems.contained_executor) (in module toil.batchSystems.kubernetes) pack_toil_uri() (in module toil.wdl.wdltoil) pad_str() (in module toil.utils.toilStats) panic (class in toil.jobStores.aws.jobStore) (class in toil.lib.ec2) (class in toil.lib.exceptions) (class in toil.test.src.miscTests) parent() (in module toil.test.src.jobTest) (in module toil.test.src.promisesTest) (in module toil.test.src.resumabilityTest) parentJob() (in module toil.test.batchSystems.batchSystemTest) parentMessage (in module toil.test.mesos.helloWorld) parse_accelerator() (in module toil.job) (in module toil.wdl.wdltoil) parse_accelerator_list() (in module toil.options.common) parse_args() (in module toil.worker) parse_bjobs_record() (toil.batchSystems.lsf.LSFBatchSystem.GridEngineThread method) parse_elapsed() (toil.batchSystems.slurm.SlurmBatchSystem.GridEngineThread method) parse_int_list() (in module toil.options.common) parse_iso_utc() (in module toil.lib.memoize) (in module toil.provisioners.node) parse_jobstore() (in module toil.options.common) parse_mem_and_cmd_from_output() (in module toil.batchSystems.lsf) (in module toil.batchSystems.lsfHelper) (in module toil.test.batchSystems.test_lsf_helper) parse_memory() (in module toil.batchSystems.lsf) (in module toil.batchSystems.lsfHelper) (in module toil.lib.ec2nodes) parse_memory_string() (in module toil.lib.conversions) parse_node_types() (in module toil.options.common) (in module toil.provisioners) (in module toil.test.provisioners.provisionerTest) (in module toil.utils.toilLaunchCluster) parse_params() (toil.server.cli.wes_cwl_runner.WESClientWithWorkflowEngineParameters method) parse_set_env() (in module toil.options.common) parse_storage() (in module toil.lib.ec2nodes) parse_str_list() (in module toil.options.common) parse_workflow_manifest_file() (in module toil.server.wes.amazon_wes_utils) parse_workflow_zip_file() (in module toil.server.wes.amazon_wes_utils) ParseableAcceleratorRequirement (in module toil.job) ParseableDivisibleResource (in module toil.job) ParseableFlag (in module toil.job) ParseableIndivisibleResource (in module toil.job) ParseableRequirement (in module toil.job) parseBjobs() (toil.batchSystems.lsf.LSFBatchSystem.GridEngineThread method) parseBool() (in module toil.options.common) parseDockerAppliance() (in module toil) (in module toil.test.src.dockerCheckTest) ParsedRequirement (in module toil.batchSystems.abstractBatchSystem) (in module toil.job) parseLocator() (toil.batchSystems.abstractBatchSystem.Toil static method) (toil.batchSystems.awsBatch.Toil static method) (toil.batchSystems.cleanup_support.Toil static method) (toil.batchSystems.kubernetes.Toil static method) (toil.batchSystems.singleMachine.Toil static method) (toil.common.Toil static method) (toil.cwl.cwltoil.Toil static method) (toil.fileStores.abstractFileStore.Toil static method) (toil.job.Toil static method) (toil.server.wes.tasks.Toil static method) (toil.test.batchSystems.batch_system_plugin_test.Toil static method) (toil.test.batchSystems.batchSystemTest.Toil static method) (toil.test.jobStores.jobStoreTest.Toil static method) (toil.test.lib.dockerTest.Toil static method) (toil.test.mesos.helloWorld.Toil static method) (toil.test.options.options.Toil static method) (toil.test.sort.restart_sort.Toil static method) (toil.test.sort.sort.Toil static method) (toil.test.sort.sortTest.Toil static method) (toil.test.src.busTest.Toil static method) (toil.test.src.environmentTest.Toil static method) (toil.test.src.fileStoreTest.Toil static method) (toil.test.src.importExportFileTest.Toil static method) (toil.test.src.jobDescriptionTest.Toil static method) (toil.test.src.jobFileStoreTest.Toil static method) (toil.test.src.jobTest.Toil static method) (toil.test.src.restartDAGTest.Toil static method) (toil.test.src.toilContextManagerTest.Toil static method) (toil.test.utils.toilKillTest.Toil static method) (toil.test.utils.utilsTest.Toil static method) (toil.utils.toilClean.Toil static method) (toil.utils.toilDebugFile.Toil static method) (toil.utils.toilDebugJob.Toil static method) (toil.utils.toilKill.Toil static method) (toil.utils.toilStats.Toil static method) (toil.utils.toilStatus.Toil static method) (toil.wdl.wdltoil.Toil static method) (toil.worker.Toil static method) parseMaxMem() (toil.batchSystems.lsf.LSFBatchSystem.GridEngineThread method) parser (in module toil.test.provisioners.restartScript) parser_with_common_options() (in module toil.common) (in module toil.utils.toilClean) (in module toil.utils.toilDebugFile) (in module toil.utils.toilDebugJob) (in module toil.utils.toilDestroyCluster) (in module toil.utils.toilKill) (in module toil.utils.toilLaunchCluster) (in module toil.utils.toilRsyncCluster) (in module toil.utils.toilSshCluster) (in module toil.utils.toilStats) (in module toil.utils.toilStatus) parser_with_server_options() (in module toil.server.app) PARTITION (toil.batchSystems.abstractBatchSystem.BatchJobExitReason attribute) (toil.batchSystems.abstractGridEngineBatchSystem.BatchJobExitReason attribute) (toil.batchSystems.awsBatch.BatchJobExitReason attribute) (toil.batchSystems.kubernetes.BatchJobExitReason attribute) (toil.batchSystems.lsf.BatchJobExitReason attribute) (toil.batchSystems.mesos.batchSystem.BatchJobExitReason attribute) (toil.batchSystems.slurm.BatchJobExitReason attribute) (toil.leader.BatchJobExitReason attribute) (toil.test.batchSystems.test_slurm.BatchJobExitReason attribute) (toil.test.src.busTest.BatchJobExitReason attribute) passingFn() (in module toil.test.src.restartDAGTest) path_to_loc() (in module toil.cwl.cwltoil) PathIndexingPromiseTest (class in toil.test.src.promisesTest) per_core_reservation() (in module toil.batchSystems.lsf) (in module toil.batchSystems.lsfHelper) per_core_reserve_from_stream() (in module toil.batchSystems.lsfHelper) PerfectServiceTest (class in toil.test.src.jobServiceTest) permission_matches_any() (in module toil.lib.aws.iam) physicalDisk() (in module toil) physicalMemory (toil.batchSystems.local_support.SingleMachineBatchSystem attribute) (toil.batchSystems.singleMachine.SingleMachineBatchSystem attribute) (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystem attribute) (toil.test.src.jobServiceTest.SingleMachineBatchSystem attribute) physicalMemory() (in module toil) pick_value() (toil.cwl.cwltoil.ResolveSource method) pickle() (toil.batchSystems.abstractBatchSystem.Resource method) (toil.batchSystems.awsBatch.Resource method) (toil.batchSystems.contained_executor.Resource method) (toil.batchSystems.kubernetes.Resource method) (toil.batchSystems.mesos.executor.Resource method) (toil.resource.Resource method) (toil.test.src.resourceTest.Resource method) pip() (toil.test.cactus.test_cactus_integration.AbstractClusterTest method) (toil.test.provisioners.aws.awsProvisionerTest.AbstractClusterTest method) (toil.test.provisioners.clusterTest.AbstractClusterTest method) (toil.test.wdl.wdltoil_test_kubernetes.AbstractClusterTest method) pkg_root (in module toil.test.cwl.cwlTest) (in module toil.test.docs.scriptsTest) (in module toil.test.utils.toilKillTest) (in module toil.test.utils.utilsTest) policy_permissions_allow() (in module toil.lib.aws.iam) (in module toil.provisioners.aws.awsProvisioner) poll_run() (in module toil.server.cli.wes_cwl_runner) populate_env_vars() (toil.cwl.cwltoil.CWLJob method) postprocess() (toil.wdl.wdltoil.WDLBaseJob method) potential_absolute_uris() (in module toil.wdl.wdltoil) pre_update_hook() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) preemptable() (toil.batchSystems.abstractBatchSystem.Requirer method) (toil.batchSystems.awsBatch.Requirer method) (toil.batchSystems.kubernetes.Requirer method) (toil.batchSystems.singleMachine.Requirer method) (toil.batchSystems.slurm.Requirer method) (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.Job method) (toil.job.Requirer method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.batchSystems.batchSystemTest.Requirer method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) preemptible (in module toil.test.batchSystems.batchSystemTest) (toil.batchSystems.abstractBatchSystem.Requirer property) (toil.batchSystems.awsBatch.Requirer property) (toil.batchSystems.kubernetes.Requirer property) (toil.batchSystems.singleMachine.Requirer property) (toil.batchSystems.slurm.Requirer property) (toil.cwl.cwltoil.Job property) (toil.fileStores.abstractFileStore.Job property) (toil.fileStores.cachingFileStore.Job property) (toil.fileStores.nonCachingFileStore.Job property) (toil.job.Job property) (toil.job.RequirementsDict attribute) (toil.job.Requirer property) (toil.jobStores.aws.jobStore.Job property) (toil.test.batchSystems.batchSystemTest.Job property) (toil.test.batchSystems.batchSystemTest.Requirer property) (toil.test.jobStores.jobStoreTest.Job property) (toil.test.lib.dockerTest.Job property) (toil.test.mesos.helloWorld.Job property) (toil.test.mesos.stress.Job property) (toil.test.provisioners.restartScript.Job property) (toil.test.sort.restart_sort.Job property) (toil.test.sort.sort.Job property) (toil.test.sort.sortTest.Job property) (toil.test.src.busTest.Job property) (toil.test.src.checkpointTest.Job property) (toil.test.src.deferredFunctionTest.Job property) (toil.test.src.environmentTest.Job property) (toil.test.src.fileStoreTest.Job property) (toil.test.src.helloWorldTest.Job property) (toil.test.src.importExportFileTest.Job property) (toil.test.src.jobDescriptionTest.Job property) (toil.test.src.jobEncapsulationTest.Job property) (toil.test.src.jobFileStoreTest.Job property) (toil.test.src.jobServiceTest.Job property) (toil.test.src.jobTest.Job property) (toil.test.src.promisedRequirementTest.Job property) (toil.test.src.promisesTest.Job property) (toil.test.src.realtimeLoggerTest.Job property) (toil.test.src.restartDAGTest.Job property) (toil.test.src.resumabilityTest.Job property) (toil.test.src.retainTempDirTest.Job property) (toil.test.src.toilContextManagerTest.Job property) (toil.test.src.userDefinedJobArgTypeTest.Job property) (toil.test.utils.utilsTest.Job property) (toil.utils.toilStats.Job property) (toil.wdl.wdltoil.Job property) (toil.worker.Job property)

preemptibleCompensation (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) PreemptibleDeficitCompensationTest (class in toil.test.provisioners.aws.awsProvisionerTest) PREFIX (toil.batchSystems.abstractBatchSystem.DeferredFunctionManager attribute) (toil.deferred.DeferredFunctionManager attribute) (toil.worker.DeferredFunctionManager attribute) PREFIX_LENGTH (in module toil.test.src.jobFileStoreTest) prepare_restart() (toil.batchSystems.abstractBatchSystem.Config method) (toil.batchSystems.awsBatch.Config method) (toil.batchSystems.cleanup_support.Config method) (toil.batchSystems.kubernetes.Config method) (toil.batchSystems.local_support.Config method) (toil.batchSystems.singleMachine.Config method) (toil.common.Config method) (toil.job.Config method) (toil.jobStores.abstractJobStore.Config method) (toil.leader.Config method) (toil.provisioners.clusterScaler.Config method) (toil.test.batchSystems.batchSystemTest.Config method) (toil.test.batchSystems.test_slurm.Config method) (toil.test.jobStores.jobStoreTest.Config method) (toil.test.provisioners.clusterScalerTest.Config method) (toil.test.src.workerTest.Config method) (toil.test.utils.utilsTest.Config method) (toil.utils.toilDebugFile.Config method) (toil.utils.toilDebugJob.Config method) (toil.utils.toilKill.Config method) (toil.utils.toilStats.Config method) (toil.utils.toilStatus.Config method) (toil.worker.Config method) prepare_start() (toil.batchSystems.abstractBatchSystem.Config method) (toil.batchSystems.awsBatch.Config method) (toil.batchSystems.cleanup_support.Config method) (toil.batchSystems.kubernetes.Config method) (toil.batchSystems.local_support.Config method) (toil.batchSystems.singleMachine.Config method) (toil.common.Config method) (toil.job.Config method) (toil.jobStores.abstractJobStore.Config method) (toil.leader.Config method) (toil.provisioners.clusterScaler.Config method) (toil.test.batchSystems.batchSystemTest.Config method) (toil.test.batchSystems.test_slurm.Config method) (toil.test.jobStores.jobStoreTest.Config method) (toil.test.provisioners.clusterScalerTest.Config method) (toil.test.src.workerTest.Config method) (toil.test.utils.utilsTest.Config method) (toil.utils.toilDebugFile.Config method) (toil.utils.toilDebugJob.Config method) (toil.utils.toilKill.Config method) (toil.utils.toilStats.Config method) (toil.utils.toilStatus.Config method) (toil.worker.Config method) prepareBsub() (toil.batchSystems.lsf.LSFBatchSystem.GridEngineThread method) prepareForPromiseRegistration() (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.EncapsulatedJob method) (toil.job.Job method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) prepareQsub() (toil.batchSystems.gridengine.GridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.torque.TorqueBatchSystem.GridEngineThread method) prepareSbatch() (toil.batchSystems.slurm.SlurmBatchSystem.GridEngineThread method) prepareSubmission() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.gridengine.GridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.htcondor.HTCondorBatchSystem.GridEngineThread method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.lsf.LSFBatchSystem.GridEngineThread method) (toil.batchSystems.slurm.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.slurm.SlurmBatchSystem.GridEngineThread method) (toil.batchSystems.torque.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.torque.TorqueBatchSystem.GridEngineThread method) prepareSystem() (toil.batchSystems.abstractBatchSystem.Resource class method) (toil.batchSystems.awsBatch.Resource class method) (toil.batchSystems.contained_executor.Resource class method) (toil.batchSystems.kubernetes.Resource class method) (toil.batchSystems.mesos.executor.Resource class method) (toil.resource.Resource class method) (toil.test.src.resourceTest.Resource class method) presenceIndicator() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo class method) (toil.jobStores.aws.jobStore.SDBHelper class method) (toil.jobStores.aws.utils.SDBHelper class method) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo class method) pretty_space() (in module toil.utils.toilStats) pretty_time() (in module toil.utils.toilStats) previousVersion (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo property) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo property) print_bus_messages() (toil.test.utils.utilsTest.ToilStatus method) (toil.utils.toilDebugJob.ToilStatus method) (toil.utils.toilStatus.ToilStatus method) print_dot_chart() (toil.test.utils.utilsTest.ToilStatus method) (toil.utils.toilDebugJob.ToilStatus method) (toil.utils.toilStatus.ToilStatus method) print_logs_and_exit() (in module toil.server.cli.wes_cwl_runner) printAggregateJobStats() (toil.test.utils.utilsTest.ToilStatus method) (toil.utils.toilDebugJob.ToilStatus method) (toil.utils.toilStatus.ToilStatus method) printContentsOfJobStore() (in module toil.utils.toilDebugFile) (in module toil.utils.toilDebugJob) printHelp() (in module toil.utils.toilMain) printJobChildren() (toil.test.utils.utilsTest.ToilStatus method) (toil.utils.toilDebugJob.ToilStatus method) (toil.utils.toilStatus.ToilStatus method) printJobLog() (toil.test.utils.utilsTest.ToilStatus method) (toil.utils.toilDebugJob.ToilStatus method) (toil.utils.toilStatus.ToilStatus method) printq() (in module toil.lib.aws.utils) (in module toil.lib.misc) printUnicodeCharacter() (in module toil.test.utils.utilsTest) printVersion() (in module toil.utils.toilMain) process_data() (in module toil.test.utils.utilsTest) (in module toil.utils.toilStats) process_finished_job() (toil.leader.Leader method) process_finished_job_description() (toil.leader.Leader method) process_name_exists() (in module toil.fileStores.cachingFileStore) (in module toil.fileStores.nonCachingFileStore) (in module toil.lib.threading) processRemovedJob() (toil.leader.Leader method) processTotallyFailedJob() (toil.leader.Leader method) ProcessType (in module toil.cwl.cwltoil) prohibited_labels (toil.batchSystems.kubernetes.KubernetesBatchSystem.Placement attribute) projectID (toil.test.jobStores.jobStoreTest.GoogleJobStoreTest attribute) (toil.test.provisioners.gceProvisionerTest.AbstractGCEAutoscaleTest attribute) Promise (class in toil.cwl.cwltoil) (class in toil.job) (class in toil.wdl.wdltoil) promise_tuples (toil.cwl.cwltoil.ResolveSource attribute) Promised (in module toil.cwl.cwltoil) (in module toil.job) (in module toil.wdl.wdltoil) PromisedRequirement (class in toil.job) (class in toil.test.src.promisedRequirementTest) PromisedRequirementFunctionWrappingJob (class in toil.job) PromisedRequirementJobFunctionWrappingJob (class in toil.job) provisioner (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) ProvisionerTest (class in toil.test.provisioners.provisionerTest) ProxyConnectionError prune() (in module toil.lib.ec2) publicUrlExpiration (toil.cwl.cwltoil.AbstractJobStore attribute) (toil.cwl.utils.AbstractJobStore attribute) (toil.fileStores.abstractFileStore.AbstractJobStore attribute) (toil.fileStores.cachingFileStore.AbstractJobStore attribute) (toil.fileStores.nonCachingFileStore.AbstractJobStore attribute) (toil.jobStores.abstractJobStore.AbstractJobStore attribute) (toil.jobStores.aws.jobStore.AbstractJobStore attribute) (toil.jobStores.fileJobStore.AbstractJobStore attribute) (toil.jobStores.googleJobStore.AbstractJobStore attribute) (toil.leader.AbstractJobStore attribute) (toil.serviceManager.AbstractJobStore attribute) (toil.toilState.AbstractJobStore attribute) (toil.utils.toilStats.AbstractJobStore attribute) (toil.wdl.wdltoil.AbstractJobStore attribute) (toil.worker.AbstractJobStore attribute) publish() (toil.batchSystems.abstractBatchSystem.MessageBus method) (toil.batchSystems.abstractBatchSystem.MessageOutbox method) (toil.bus.MessageBus method) (toil.bus.MessageOutbox method) (toil.common.MessageBus method) (toil.test.src.busTest.MessageBus method) (toil.toilState.MessageBus method) put_client() (toil.leader.ServiceManager method) (toil.serviceManager.ServiceManager method) putScript() (toil.test.provisioners.aws.awsProvisionerTest.AbstractAWSAutoscaleTest method) python (in module toil.test.docs.scriptsTest) (in module toil.test.utils.toilDebugTest) (in module toil.test.utils.utilsTest) (in module toil.version) python() (toil.test.cactus.test_cactus_integration.AbstractClusterTest method) (toil.test.provisioners.aws.awsProvisionerTest.AbstractClusterTest method) (toil.test.provisioners.clusterTest.AbstractClusterTest method) (toil.test.wdl.wdltoil_test_kubernetes.AbstractClusterTest method)

Q

queue_run() (toil.server.wes.toil_backend.ToilWorkflow method) queue_size (toil.bus.QueueSizeMessage attribute) (toil.common.QueueSizeMessage attribute) (toil.leader.QueueSizeMessage attribute)

QueueSizeMessage (class in toil.bus) (class in toil.common) (class in toil.leader)

R

R (toil.batchSystems.kubernetes.KubernetesBatchSystem attribute) r3_8xlarge (in module toil.test.provisioners.clusterScalerTest) r5_2xlarge (in module toil.test.provisioners.clusterScalerTest) r5_4xlarge (in module toil.test.provisioners.clusterScalerTest) raise_() (in module toil.lib.exceptions) (in module toil.lib.threading) (in module toil.test.src.miscTests) reachable() (toil.test.src.jobTest.JobTest method) read_cache() (toil.server.utils.AbstractStateStore method) (toil.server.utils.WorkflowStateStore method) read_file() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) read_file_stream() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) read_from_url() (toil.cwl.cwltoil.AbstractJobStore class method) (toil.cwl.utils.AbstractJobStore class method) (toil.fileStores.abstractFileStore.AbstractJobStore class method) (toil.fileStores.cachingFileStore.AbstractJobStore class method) (toil.fileStores.nonCachingFileStore.AbstractJobStore class method) (toil.jobStores.abstractJobStore.AbstractJobStore class method) (toil.jobStores.aws.jobStore.AbstractJobStore class method) (toil.jobStores.fileJobStore.AbstractJobStore class method) (toil.jobStores.googleJobStore.AbstractJobStore class method) (toil.leader.AbstractJobStore class method) (toil.serviceManager.AbstractJobStore class method) (toil.toilState.AbstractJobStore class method) (toil.utils.toilStats.AbstractJobStore class method) (toil.wdl.wdltoil.AbstractJobStore class method) (toil.worker.AbstractJobStore class method) read_kill_flag() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) read_leader_node_id() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) read_leader_pid() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) read_logs() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) read_shared_file_stream() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) ReadablePipe (class in toil.jobStores.aws.jobStore) (class in toil.jobStores.googleJobStore) (class in toil.jobStores.utils) ReadableTransformingPipe (class in toil.jobStores.aws.jobStore) (class in toil.jobStores.utils) readClusterSettings() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AWSProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.provisioners.gceProvisioner.GCEProvisioner method) (toil.test.provisioners.aws.awsProvisionerTest.AWSProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method) readFile() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) readFileStream() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) readFrom() (toil.jobStores.aws.jobStore.WritablePipe method) (toil.jobStores.googleJobStore.WritablePipe method) (toil.jobStores.utils.WritablePipe method) readGlobalFile() (toil.batchSystems.abstractBatchSystem.AbstractFileStore method) (toil.cwl.cwltoil.AbstractFileStore method) (toil.cwl.utils.AbstractFileStore method) (toil.fileStores.abstractFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.CachingFileStore method) (toil.fileStores.nonCachingFileStore.AbstractFileStore method) (toil.fileStores.nonCachingFileStore.NonCachingFileStore method) (toil.test.cwl.cwlTest.AbstractFileStore method) (toil.wdl.wdltoil.AbstractFileStore method) (toil.worker.AbstractFileStore method) readGlobalFileMutableByDefault (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) readGlobalFileStream() (toil.batchSystems.abstractBatchSystem.AbstractFileStore method) (toil.cwl.cwltoil.AbstractFileStore method) (toil.cwl.utils.AbstractFileStore method) (toil.fileStores.abstractFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.CachingFileStore method) (toil.fileStores.nonCachingFileStore.AbstractFileStore method) (toil.fileStores.nonCachingFileStore.NonCachingFileStore method) (toil.test.cwl.cwlTest.AbstractFileStore method) (toil.wdl.wdltoil.AbstractFileStore method) (toil.worker.AbstractFileStore method) readSharedFileStream() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) readStatsAndLogging() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) readStatsFileOwnerID (toil.jobStores.aws.jobStore.AWSJobStore attribute) (toil.test.lib.aws.test_s3.AWSJobStore attribute) real_id() (toil.test.wdl.wdltoil_test.WDLWorkflowGraph method) (toil.wdl.wdltoil.WDLWorkflowGraph method) realpath() (toil.cwl.cwltoil.ToilFsAccess method) RealtimeLogger (class in toil.common) (class in toil.deferred) (class in toil.realtimeLogger) (class in toil.test.sort.restart_sort) (class in toil.test.sort.sort) (class in toil.test.src.fileStoreTest) (class in toil.test.src.realtimeLoggerTest) RealtimeLoggerMetaclass (class in toil.realtimeLogger) RealtimeLoggerTest (class in toil.test.src.realtimeLoggerTest) realTimeLogging (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) record_extra_cpu() (toil.job.ResourceMonitor class method) (toil.lib.resources.ResourceMonitor class method) (toil.statsAndLogging.ResourceMonitor class method) (toil.wdl.wdltoil.ResourceMonitor class method) (toil.worker.ResourceMonitor class method) record_extra_memory() (toil.job.ResourceMonitor class method) (toil.lib.resources.ResourceMonitor class method) (toil.statsAndLogging.ResourceMonitor class method) (toil.wdl.wdltoil.ResourceMonitor class method) (toil.worker.ResourceMonitor class method) recursive_dependencies() (in module toil.wdl.wdltoil) reduce_region_json_size() (in module toil.lib.ec2nodes) refresh() (toil.batchSystems.abstractBatchSystem.Resource method) (toil.batchSystems.awsBatch.Resource method) (toil.batchSystems.contained_executor.Resource method) (toil.batchSystems.kubernetes.Resource method) (toil.batchSystems.mesos.executor.Resource method) (toil.resource.Resource method) (toil.test.src.resourceTest.Resource method) region (toil.test.server.serverTest.BucketUsingTest attribute) region_json_dirname (in module toil.lib.ec2nodes) region_to_bucket_location() (in module toil.lib.aws.utils) regionDict (in module toil.lib.generatedEC2Lists) register() (toil.batchSystems.abstractBatchSystem.Resource method) (toil.batchSystems.awsBatch.Resource method) (toil.batchSystems.contained_executor.Resource method) (toil.batchSystems.kubernetes.Resource method) (toil.batchSystems.mesos.executor.Resource method) (toil.resource.Resource method) (toil.test.src.resourceTest.Resource method) registered() (toil.batchSystems.mesos.batchSystem.MesosBatchSystem method) (toil.batchSystems.mesos.executor.MesosExecutor method) registerPromise() (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.Job method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) RegularLogTest (class in toil.test.src.regularLogTest) reissueMissingJobs() (toil.leader.Leader method) reissueOverLongJobs() (toil.leader.Leader method) release() (toil.batchSystems.abstractBatchSystem.ResourcePool method) (toil.batchSystems.abstractBatchSystem.ResourceSet method) (toil.batchSystems.kubernetes.ResourcePool method) (toil.batchSystems.singleMachine.ResourcePool method) (toil.batchSystems.singleMachine.ResourceSet method) remainingBillingInterval() (toil.provisioners.abstractProvisioner.Node method) (toil.provisioners.aws.awsProvisioner.Node method) (toil.provisioners.gceProvisioner.Node method) (toil.provisioners.node.Node method) (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method) (toil.test.provisioners.clusterScalerTest.Node method) remainingTryCount (toil.batchSystems.abstractBatchSystem.JobDescription property) (toil.batchSystems.awsBatch.JobDescription property) (toil.batchSystems.kubernetes.JobDescription property) (toil.batchSystems.local_support.JobDescription property) (toil.batchSystems.mesos.batchSystem.JobDescription property) (toil.batchSystems.singleMachine.JobDescription property) (toil.fileStores.abstractFileStore.JobDescription property) (toil.fileStores.cachingFileStore.JobDescription property) (toil.fileStores.nonCachingFileStore.JobDescription property) (toil.job.JobDescription property) (toil.jobStores.abstractJobStore.JobDescription property) (toil.jobStores.aws.jobStore.JobDescription property) (toil.leader.JobDescription property) (toil.provisioners.clusterScaler.JobDescription property) (toil.test.batchSystems.batch_system_plugin_test.JobDescription property) (toil.test.batchSystems.batchSystemTest.JobDescription property) (toil.test.jobStores.jobStoreTest.JobDescription property) (toil.test.provisioners.clusterScalerTest.JobDescription property) (toil.test.src.jobDescriptionTest.JobDescription property) (toil.test.src.workerTest.JobDescription property) (toil.toilState.JobDescription property) (toil.utils.toilStatus.JobDescription property) (toil.worker.JobDescription property) remove_empty_listings() (in module toil.cwl.cwltoil) remove_pickle_problems() (in module toil.cwl.cwltoil) removeJob() (toil.leader.Leader method) renameReferences() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) replace() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) replay_message_bus() (in module toil.bus) (in module toil.server.wes.toil_backend) (in module toil.test.src.busTest) (in module toil.utils.toilStatus) report() (in module toil.utils.toilStats) (toil.utils.toilStats.ColumnWidths method) report_data() (in module toil.utils.toilStats) report_number() (in module toil.utils.toilStats) report_on_jobs() (toil.test.utils.utilsTest.ToilStatus method) (toil.utils.toilDebugJob.ToilStatus method) (toil.utils.toilStatus.ToilStatus method) report_pretty_data() (in module toil.utils.toilStats) report_space() (in module toil.utils.toilStats) report_time() (in module toil.utils.toilStats) report_unit() (in module toil.utils.toilStats) report_wdl_errors() (in module toil.wdl.wdltoil) requestCheckDockerIo() (in module toil) requestCheckRegularDocker() (in module toil) required_env_vars() (toil.cwl.cwltoil.CWLJob method) required_labels (toil.batchSystems.kubernetes.KubernetesBatchSystem.Placement attribute) REQUIREMENT_NAMES (in module toil.job) requirements (toil.batchSystems.abstractBatchSystem.Requirer property) (toil.batchSystems.awsBatch.Requirer property) (toil.batchSystems.kubernetes.Requirer property) (toil.batchSystems.singleMachine.Requirer property) (toil.batchSystems.slurm.Requirer property) (toil.job.Requirer property) (toil.test.batchSystems.batchSystemTest.Requirer property) requirements_string() (toil.batchSystems.abstractBatchSystem.Requirer method) (toil.batchSystems.awsBatch.Requirer method) (toil.batchSystems.kubernetes.Requirer method) (toil.batchSystems.singleMachine.Requirer method) (toil.batchSystems.slurm.Requirer method) (toil.job.Requirer method) (toil.test.batchSystems.batchSystemTest.Requirer method) RequirementsDict (class in toil.job) Requirer (class in toil.batchSystems.abstractBatchSystem) (class in toil.batchSystems.awsBatch) (class in toil.batchSystems.kubernetes) (class in toil.batchSystems.singleMachine) (class in toil.batchSystems.slurm) (class in toil.job) (class in toil.test.batchSystems.batchSystemTest) reregistered() (toil.batchSystems.mesos.batchSystem.MesosBatchSystem method) (toil.batchSystems.mesos.executor.MesosExecutor method) rescueJobsFrequency (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute)

RESERVE_BREAKPOINTS (in module toil.provisioners.clusterScaler) RESERVE_FRACTIONS (in module toil.provisioners.clusterScaler) RESERVE_SMALL_AMOUNT (in module toil.provisioners.clusterScaler) RESERVE_SMALL_LIMIT (in module toil.provisioners.clusterScaler) reserve_versions() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) reset_job() (toil.leader.ToilState method) (toil.serviceManager.ToilState method) (toil.toilState.ToilState method) reset_job_expecting_change() (toil.leader.ToilState method) (toil.serviceManager.ToilState method) (toil.toilState.ToilState method) resetCounters() (in module toil.test.batchSystems.batchSystemTest) resolve() (toil.cwl.cwltoil.DefaultWithSource method) (toil.cwl.cwltoil.JustAValue method) (toil.cwl.cwltoil.ResolveSource method) (toil.cwl.cwltoil.StepValueFrom method) resolve_dict_w_promises() (in module toil.cwl.cwltoil) resolve_operation_id() (toil.server.wes.abstract_backend.WESBackend method) (toil.server.wes.toil_backend.WESBackend method) resolveEntryPoint() (in module toil) (in module toil.batchSystems.mesos.batchSystem) (in module toil.leader) (in module toil.test.sort.sortTest) (in module toil.test.utils.utilsTest) ResolveIndirect (class in toil.cwl.cwltoil) ResolveSource (class in toil.cwl.cwltoil) Resource (class in toil.batchSystems.abstractBatchSystem) (class in toil.batchSystems.awsBatch) (class in toil.batchSystems.contained_executor) (class in toil.batchSystems.kubernetes) (class in toil.batchSystems.mesos.executor) (class in toil.resource) (class in toil.test.src.resourceTest) resource() (in module toil.lib.aws.session) (toil.lib.aws.session.AWSConnectionManager method) (toil.provisioners.aws.awsProvisioner.AWSConnectionManager method) (toil.test.provisioners.clusterTest.AWSConnectionManager method) resourceEnvNamePrefix (toil.batchSystems.abstractBatchSystem.Resource attribute) (toil.batchSystems.awsBatch.Resource attribute) (toil.batchSystems.contained_executor.Resource attribute) (toil.batchSystems.kubernetes.Resource attribute) (toil.batchSystems.mesos.executor.Resource attribute) (toil.resource.Resource attribute) (toil.test.src.resourceTest.Resource attribute) ResourceException, [1] ResourceMonitor (class in toil.job) (class in toil.lib.resources) (class in toil.statsAndLogging) (class in toil.wdl.wdltoil) (class in toil.worker) resourceOffers() (toil.batchSystems.mesos.batchSystem.MesosBatchSystem method) ResourcePool (class in toil.batchSystems.abstractBatchSystem) (class in toil.batchSystems.kubernetes) (class in toil.batchSystems.singleMachine) ResourceSet (class in toil.batchSystems.abstractBatchSystem) (class in toil.batchSystems.singleMachine) ResourceTest (class in toil.test.src.resourceTest) restart (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) restart() (toil.batchSystems.abstractBatchSystem.Toil method) (toil.batchSystems.awsBatch.Toil method) (toil.batchSystems.cleanup_support.Toil method) (toil.batchSystems.kubernetes.Toil method) (toil.batchSystems.singleMachine.Toil method) (toil.common.Toil method) (toil.cwl.cwltoil.Toil method) (toil.fileStores.abstractFileStore.Toil method) (toil.job.Toil method) (toil.server.wes.tasks.Toil method) (toil.test.batchSystems.batch_system_plugin_test.Toil method) (toil.test.batchSystems.batchSystemTest.Toil method) (toil.test.jobStores.jobStoreTest.Toil method) (toil.test.lib.dockerTest.Toil method) (toil.test.mesos.helloWorld.Toil method) (toil.test.options.options.Toil method) (toil.test.sort.restart_sort.Toil method) (toil.test.sort.sort.Toil method) (toil.test.sort.sortTest.Toil method) (toil.test.src.busTest.Toil method) (toil.test.src.environmentTest.Toil method) (toil.test.src.fileStoreTest.Toil method) (toil.test.src.importExportFileTest.Toil method) (toil.test.src.jobDescriptionTest.Toil method) (toil.test.src.jobFileStoreTest.Toil method) (toil.test.src.jobTest.Toil method) (toil.test.src.restartDAGTest.Toil method) (toil.test.src.toilContextManagerTest.Toil method) (toil.test.utils.toilKillTest.Toil method) (toil.test.utils.utilsTest.Toil method) (toil.utils.toilClean.Toil method) (toil.utils.toilDebugFile.Toil method) (toil.utils.toilDebugJob.Toil method) (toil.utils.toilKill.Toil method) (toil.utils.toilStats.Toil method) (toil.utils.toilStatus.Toil method) (toil.wdl.wdltoil.Toil method) (toil.worker.Toil method) restartCheckpoint() (toil.job.CheckpointJobDescription method) (toil.jobStores.abstractJobStore.CheckpointJobDescription method) (toil.leader.CheckpointJobDescription method) (toil.test.src.workerTest.CheckpointJobDescription method) (toil.toilState.CheckpointJobDescription method) (toil.worker.CheckpointJobDescription method) RestartDAGTest (class in toil.test.src.restartDAGTest) RestartingJob (class in toil.test.src.importExportFileTest) restore_batch_system_plugin_state() (in module toil.batchSystems.registry) (in module toil.test.batchSystems.batchSystemTest) restore_checkpoint() (toil.job.CheckpointJobDescription method) (toil.jobStores.abstractJobStore.CheckpointJobDescription method) (toil.leader.CheckpointJobDescription method) (toil.test.src.workerTest.CheckpointJobDescription method) (toil.toilState.CheckpointJobDescription method) (toil.worker.CheckpointJobDescription method) result_status (toil.bus.JobUpdatedMessage attribute) (toil.leader.JobUpdatedMessage attribute) (toil.toilState.JobUpdatedMessage attribute) ResumabilityTest (class in toil.test.src.resumabilityTest) resume() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) resumeJobStore() (toil.batchSystems.abstractBatchSystem.Toil class method) (toil.batchSystems.awsBatch.Toil class method) (toil.batchSystems.cleanup_support.Toil class method) (toil.batchSystems.kubernetes.Toil class method) (toil.batchSystems.singleMachine.Toil class method) (toil.common.Toil class method) (toil.cwl.cwltoil.Toil class method) (toil.fileStores.abstractFileStore.Toil class method) (toil.job.Toil class method) (toil.server.wes.tasks.Toil class method) (toil.test.batchSystems.batch_system_plugin_test.Toil class method) (toil.test.batchSystems.batchSystemTest.Toil class method) (toil.test.jobStores.jobStoreTest.Toil class method) (toil.test.lib.dockerTest.Toil class method) (toil.test.mesos.helloWorld.Toil class method) (toil.test.options.options.Toil class method) (toil.test.sort.restart_sort.Toil class method) (toil.test.sort.sort.Toil class method) (toil.test.sort.sortTest.Toil class method) (toil.test.src.busTest.Toil class method) (toil.test.src.environmentTest.Toil class method) (toil.test.src.fileStoreTest.Toil class method) (toil.test.src.importExportFileTest.Toil class method) (toil.test.src.jobDescriptionTest.Toil class method) (toil.test.src.jobFileStoreTest.Toil class method) (toil.test.src.jobTest.Toil class method) (toil.test.src.restartDAGTest.Toil class method) (toil.test.src.toilContextManagerTest.Toil class method) (toil.test.utils.toilKillTest.Toil class method) (toil.test.utils.utilsTest.Toil class method) (toil.utils.toilClean.Toil class method) (toil.utils.toilDebugFile.Toil class method) (toil.utils.toilDebugJob.Toil class method) (toil.utils.toilKill.Toil class method) (toil.utils.toilStats.Toil class method) (toil.utils.toilStatus.Toil class method) (toil.wdl.wdltoil.Toil class method) (toil.worker.Toil class method) retry() (in module toil) (in module toil.batchSystems.awsBatch) (in module toil.batchSystems.htcondor) (in module toil.batchSystems.kubernetes) (in module toil.batchSystems.mesos.test) (in module toil.common) (in module toil.fileStores.cachingFileStore) (in module toil.fileStores.nonCachingFileStore) (in module toil.jobStores.abstractJobStore) (in module toil.jobStores.aws.jobStore) (in module toil.jobStores.aws.utils) (in module toil.lib.aws.ami) (in module toil.lib.aws.utils) (in module toil.lib.ec2) (in module toil.lib.retry) (in module toil.provisioners.aws.awsProvisioner) (in module toil.resource) (in module toil.server.utils) (in module toil.test.jobStores.jobStoreTest) (in module toil.test.provisioners.clusterTest) (in module toil.test.src.dockerCheckTest) retry_ec2() (in module toil.lib.ec2) retry_flaky_test (in module toil.lib.retry) (in module toil.test.batchSystems.batchSystemTest) (in module toil.test.src.jobServiceTest) (in module toil.test.src.promisedRequirementTest) retry_s3() (in module toil.jobStores.aws.jobStore) (in module toil.lib.aws.utils) retry_sdb() (in module toil.jobStores.aws.jobStore) (in module toil.jobStores.aws.utils) retryable_kubernetes_errors (in module toil.batchSystems.kubernetes) retryable_s3_errors() (in module toil.jobStores.aws.jobStore) (in module toil.lib.aws.utils) retryable_sdb_errors() (in module toil.jobStores.aws.utils) retryable_ssl_error() (in module toil.jobStores.aws.utils) retryCount (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) retryPredicate() (toil.leader.AbstractProvisioner static method) (toil.provisioners.abstractProvisioner.AbstractProvisioner static method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner static method) (toil.provisioners.aws.awsProvisioner.AWSProvisioner static method) (toil.provisioners.clusterScaler.AbstractProvisioner static method) (toil.provisioners.gceProvisioner.AbstractProvisioner static method) (toil.provisioners.gceProvisioner.GCEProvisioner static method) (toil.test.provisioners.aws.awsProvisionerTest.AWSProvisioner static method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner static method) return_status_code() (in module toil.lib.retry) revsort() (toil.test.cwl.cwlTest.CWLWorkflowTest method) revsort_no_checksum() (toil.test.cwl.cwlTest.CWLWorkflowTest method) RM (in module toil.lib.docker) (in module toil.test.lib.dockerTest) rm_unprocessed_secondary_files() (in module toil.cwl.cwltoil) robust_rmtree() (in module toil.deferred) (in module toil.fileStores.cachingFileStore) (in module toil.fileStores.nonCachingFileStore) (in module toil.jobStores.fileJobStore) (in module toil.lib.io) (in module toil.lib.threading) root_logger (in module toil.lib.bioio) (in module toil.statsAndLogging) (in module toil.test.sort.sortTest) rootDir (toil.test.cwl.cwlTest.CWLv11Test attribute) (toil.test.cwl.cwlTest.CWLv12Test attribute) rootDirPathEnvName (toil.batchSystems.abstractBatchSystem.Resource attribute) (toil.batchSystems.awsBatch.Resource attribute) (toil.batchSystems.contained_executor.Resource attribute) (toil.batchSystems.kubernetes.Resource attribute) (toil.batchSystems.mesos.executor.Resource attribute) (toil.resource.Resource attribute) (toil.test.src.resourceTest.Resource attribute) rootJobStoreIDFileName (toil.cwl.cwltoil.AbstractJobStore attribute) (toil.cwl.utils.AbstractJobStore attribute) (toil.fileStores.abstractFileStore.AbstractJobStore attribute) (toil.fileStores.cachingFileStore.AbstractJobStore attribute) (toil.fileStores.nonCachingFileStore.AbstractJobStore attribute) (toil.jobStores.abstractJobStore.AbstractJobStore attribute) (toil.jobStores.aws.jobStore.AbstractJobStore attribute) (toil.jobStores.fileJobStore.AbstractJobStore attribute) (toil.jobStores.googleJobStore.AbstractJobStore attribute) (toil.leader.AbstractJobStore attribute) (toil.serviceManager.AbstractJobStore attribute) (toil.toilState.AbstractJobStore attribute) (toil.utils.toilStats.AbstractJobStore attribute) (toil.wdl.wdltoil.AbstractJobStore attribute) (toil.worker.AbstractJobStore attribute) rsync_util() (toil.test.cactus.test_cactus_integration.AbstractClusterTest method) (toil.test.provisioners.aws.awsProvisionerTest.AbstractClusterTest method) (toil.test.provisioners.clusterTest.AbstractClusterTest method) (toil.test.wdl.wdltoil_test_kubernetes.AbstractClusterTest method) rsyncUtil() (toil.test.provisioners.aws.awsProvisionerTest.AbstractAWSAutoscaleTest method) (toil.test.provisioners.gceProvisionerTest.AbstractGCEAutoscaleTest method) RT (in module toil.lib.retry) run() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.mesos.test.ExceptionalThread method) (toil.batchSystems.slurm.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.torque.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.cwl.cwltoil.CWLGather method) (toil.cwl.cwltoil.CWLJob method) (toil.cwl.cwltoil.CWLJobWrapper method) (toil.cwl.cwltoil.CWLScatter method) (toil.cwl.cwltoil.CWLWorkflow method) (toil.cwl.cwltoil.ExceptionalThread method) (toil.cwl.cwltoil.Job method) (toil.cwl.cwltoil.ResolveIndirect method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.FunctionWrappingJob method) (toil.job.Job method) (toil.job.JobFunctionWrappingJob method) (toil.job.PromisedRequirementFunctionWrappingJob method) (toil.job.PromisedRequirementJobFunctionWrappingJob method) (toil.job.ServiceHostJob method) (toil.jobStores.aws.jobStore.Job method) (toil.jobStores.utils.ExceptionalThread method) (toil.leader.Leader method) (toil.lib.threading.ExceptionalThread method) (toil.provisioners.clusterScaler.ExceptionalThread method) (toil.server.wes.tasks.MultiprocessingTaskRunner class method) (toil.server.wes.tasks.TaskRunner static method) (toil.server.wes.tasks.ToilWorkflowRunner method) (toil.server.wes.toil_backend.MultiprocessingTaskRunner class method) (toil.server.wes.toil_backend.TaskRunner static method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.ExceptionalThread method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.HelloWorldFollowOn method) (toil.test.mesos.stress.HelloWorldJob method) (toil.test.mesos.stress.Job method) (toil.test.mesos.stress.LongTestFollowOn method) (toil.test.mesos.stress.LongTestJob method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.AlwaysFail method) (toil.test.src.checkpointTest.CheckpointFailsFirstTime method) (toil.test.src.checkpointTest.CheckRetryCount method) (toil.test.src.checkpointTest.FailOnce method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.FollowOn method) (toil.test.src.helloWorldTest.HelloWorld method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.importExportFileTest.RestartingJob method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.jobTest.JobFunctionWrappingJob method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.realtimeLoggerTest.LogTest method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.FollowOn method) (toil.test.src.toilContextManagerTest.HelloWorld method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.JobClass method) (toil.test.utils.utilsTest.Job method) (toil.test.utils.utilsTest.RunTwoJobsPerWorker method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.wdl.wdltoil.WDLArrayBindingsJob method) (toil.wdl.wdltoil.WDLBaseJob method) (toil.wdl.wdltoil.WDLCombineBindingsJob method) (toil.wdl.wdltoil.WDLConditionalJob method) (toil.wdl.wdltoil.WDLOutputsJob method) (toil.wdl.wdltoil.WDLRootJob method) (toil.wdl.wdltoil.WDLScatterJob method) (toil.wdl.wdltoil.WDLTaskJob method) (toil.wdl.wdltoil.WDLTaskWrapperJob method) (toil.wdl.wdltoil.WDLWorkflowJob method) (toil.wdl.wdltoil.WDLWorkflowNodeJob method) (toil.wdl.wdltoil.WDLWorkflowNodeListJob method) (toil.worker.Job method) run1000JobsOnMicros() (toil.test.provisioners.clusterScalerTest.BinPackingTest method) run_app() (in module toil.server.app) (in module toil.server.wsgi_app) run_conformance_tests() (in module toil.test.cwl.cwlTest) run_jobs() (toil.cwl.cwltoil.ToilSingleJobExecutor method) run_local_jobs_on_workers (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) run_wes (in module toil.server.wes.tasks) run_wes_task() (in module toil.server.wes.tasks) run_with_engine_options() (toil.server.cli.wes_cwl_runner.WESClientWithWorkflowEngineParameters method) run_workflow() (toil.server.app.ToilBackend method) (toil.server.wes.abstract_backend.WESBackend method) (toil.server.wes.toil_backend.ToilBackend method) (toil.server.wes.toil_backend.WESBackend method) run_zip_workflow() (toil.test.server.serverTest.ToilWESServerWorkflowTest method) runCheckpointVertexTest() (toil.test.src.jobTest.JobTest method) runMain() (in module toil.test.sort.sortTest) runNewCheckpointIsLeafVertexTest() (toil.test.src.jobTest.JobTest method) running_on_ec2() (in module toil.lib.aws) (in module toil.server.app) running_on_ecs() (in module toil.lib.aws) (in module toil.server.app) runOnAppliance() (toil.test.ApplianceTestSupport.Appliance method) (toil.test.src.autoDeploymentTest.ApplianceTestSupport.Appliance method) runToil() (toil.test.src.jobServiceTest.JobServiceTest method) (toil.test.src.jobServiceTest.PerfectServiceTest method) RunTwoJobsPerWorker (class in toil.test.utils.utilsTest) rv() (toil.cwl.cwltoil.Job method) (toil.cwl.cwltoil.SelfJob method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.EncapsulatedJob method) (toil.job.Job method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method)

S

s3_boto3_client (in module toil.jobStores.aws.jobStore) s3_boto3_resource (in module toil.jobStores.aws.jobStore) s3_resource (toil.test.lib.aws.test_s3.S3Test attribute) (toil.test.server.serverTest.BucketUsingTest attribute) S3StateStore (class in toil.server.utils) S3Test (class in toil.test.lib.aws.test_s3) safe_read_file() (in module toil.server.utils) safe_write_file() (in module toil.server.utils) safeUnpickleFromStream() (in module toil.common) (in module toil.job) (in module toil.jobStores.abstractJobStore) (in module toil.worker) save() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo method) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo method) save_batch_system_plugin_state() (in module toil.batchSystems.registry) (in module toil.test.batchSystems.batchSystemTest) saveAsResourceTo() (toil.deferred.ModuleDescriptor method) (toil.job.ModuleDescriptor method) (toil.resource.ModuleDescriptor method) (toil.test.src.jobDescriptionTest.ModuleDescriptor method) (toil.test.src.resourceTest.ModuleDescriptor method) saveAsRootJob() (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.Job method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) saveBody() (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.Job method) (toil.job.ServiceHostJob method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) scale (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) scale() (toil.batchSystems.abstractBatchSystem.Requirer method) (toil.batchSystems.awsBatch.Requirer method) (toil.batchSystems.kubernetes.Requirer method) (toil.batchSystems.singleMachine.Requirer method) (toil.batchSystems.slurm.Requirer method) (toil.job.Requirer method) (toil.test.batchSystems.batchSystemTest.Requirer method) scaleInterval (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) ScalerThread (class in toil.leader) (class in toil.provisioners.clusterScaler) (class in toil.test.provisioners.clusterScalerTest) ScalerThreadTest (class in toil.test.provisioners.clusterScalerTest) scan_bus_messages() (toil.batchSystems.abstractBatchSystem.MessageBus class method) (toil.bus.MessageBus class method) (toil.common.MessageBus class method) (toil.test.src.busTest.MessageBus class method) (toil.toilState.MessageBus class method) scan_for_unsupported_requirements() (in module toil.cwl.cwltoil) schedd_lock (in module toil.batchSystems.htcondor) script() (toil.test.provisioners.aws.awsProvisionerTest.AbstractAWSAutoscaleTest method) scriptCommand() (toil.test.batchSystems.batchSystemTest.MaxCoresSingleMachineBatchSystemTest method) sdb_unavailable() (in module toil.jobStores.aws.jobStore) (in module toil.jobStores.aws.utils) SDBHelper (class in toil.jobStores.aws.jobStore) (class in toil.jobStores.aws.utils) secure_path() (toil.server.wes.abstract_backend.WESBackend static method) (toil.server.wes.toil_backend.WESBackend static method) SelfJob (class in toil.cwl.cwltoil) send_cancel() (toil.server.utils.WorkflowStateMachine method) (toil.server.wes.tasks.WorkflowStateMachine method) (toil.server.wes.toil_backend.WorkflowStateMachine method) send_canceled() (toil.server.utils.WorkflowStateMachine method) (toil.server.wes.tasks.WorkflowStateMachine method) (toil.server.wes.toil_backend.WorkflowStateMachine method) send_complete() (toil.server.utils.WorkflowStateMachine method) (toil.server.wes.tasks.WorkflowStateMachine method) (toil.server.wes.toil_backend.WorkflowStateMachine method) send_enqueue() (toil.server.utils.WorkflowStateMachine method) (toil.server.wes.tasks.WorkflowStateMachine method) (toil.server.wes.toil_backend.WorkflowStateMachine method) send_executor_error() (toil.server.utils.WorkflowStateMachine method) (toil.server.wes.tasks.WorkflowStateMachine method) (toil.server.wes.toil_backend.WorkflowStateMachine method) send_initialize() (toil.server.utils.WorkflowStateMachine method) (toil.server.wes.tasks.WorkflowStateMachine method) (toil.server.wes.toil_backend.WorkflowStateMachine method) send_run() (toil.server.utils.WorkflowStateMachine method) (toil.server.wes.tasks.WorkflowStateMachine method) (toil.server.wes.toil_backend.WorkflowStateMachine method) send_system_error() (toil.server.utils.WorkflowStateMachine method) (toil.server.wes.tasks.WorkflowStateMachine method) (toil.server.wes.toil_backend.WorkflowStateMachine method) ServerSideCopyProhibitedError, [1] serverThread (toil.common.RealtimeLogger attribute) (toil.deferred.RealtimeLogger attribute) (toil.realtimeLogger.RealtimeLogger attribute) (toil.test.sort.restart_sort.RealtimeLogger attribute) (toil.test.sort.sort.RealtimeLogger attribute) (toil.test.src.fileStoreTest.RealtimeLogger attribute) (toil.test.src.realtimeLoggerTest.RealtimeLogger attribute) Service (class in toil.test.batchSystems.batchSystemTest) serviceAccessor() (in module toil.test.src.jobServiceTest) serviceHostIDsInBatches() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) ServiceHostJob (class in toil.job) ServiceJobDescription (class in toil.job) (class in toil.jobStores.abstractJobStore) (class in toil.leader) (class in toil.provisioners.clusterScaler) (class in toil.serviceManager) (class in toil.utils.toilStatus) ServiceManager (class in toil.leader) (class in toil.serviceManager) servicePollingInterval (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) services (toil.batchSystems.abstractBatchSystem.JobDescription property) (toil.batchSystems.awsBatch.JobDescription property) (toil.batchSystems.kubernetes.JobDescription property) (toil.batchSystems.local_support.JobDescription property) (toil.batchSystems.mesos.batchSystem.JobDescription property) (toil.batchSystems.singleMachine.JobDescription property) (toil.fileStores.abstractFileStore.JobDescription property) (toil.fileStores.cachingFileStore.JobDescription property) (toil.fileStores.nonCachingFileStore.JobDescription property) (toil.job.JobDescription property) (toil.jobStores.abstractJobStore.JobDescription property) (toil.jobStores.aws.jobStore.JobDescription property) (toil.leader.JobDescription property) (toil.provisioners.clusterScaler.JobDescription property) (toil.test.batchSystems.batch_system_plugin_test.JobDescription property) (toil.test.batchSystems.batchSystemTest.JobDescription property) (toil.test.jobStores.jobStoreTest.JobDescription property) (toil.test.provisioners.clusterScalerTest.JobDescription property) (toil.test.src.jobDescriptionTest.JobDescription property) (toil.test.src.workerTest.JobDescription property) (toil.toilState.JobDescription property) (toil.utils.toilStatus.JobDescription property) (toil.worker.JobDescription property) services_are_starting() (toil.leader.ServiceManager method) (toil.serviceManager.ServiceManager method) serviceTest() (in module toil.test.src.jobServiceTest) serviceTestParallelRecursive() (in module toil.test.src.jobServiceTest) serviceTestRecursive() (in module toil.test.src.jobServiceTest) serviceWorker() (toil.test.src.jobServiceTest.ToyService static method) session() (toil.lib.aws.session.AWSConnectionManager method) (toil.provisioners.aws.awsProvisioner.AWSConnectionManager method) (toil.test.provisioners.clusterTest.AWSConnectionManager method) set() (toil.server.utils.AbstractStateStore method) (toil.server.utils.FileStateStore method) (toil.server.utils.MemoryStateCache method) (toil.server.utils.S3StateStore method) (toil.server.utils.WorkflowStateStore method) set_batchsystem_options() (in module toil.batchSystems.options) (in module toil.common) set_checkpoint() (toil.job.CheckpointJobDescription method) (toil.jobStores.abstractJobStore.CheckpointJobDescription method) (toil.leader.CheckpointJobDescription method) (toil.test.src.workerTest.CheckpointJobDescription method) (toil.toilState.CheckpointJobDescription method) (toil.worker.CheckpointJobDescription method) set_debug_flag() (toil.cwl.cwltoil.Job method) (toil.fileStores.abstractFileStore.Job method) (toil.fileStores.cachingFileStore.Job method) (toil.fileStores.nonCachingFileStore.Job method) (toil.job.Job method) (toil.jobStores.aws.jobStore.Job method) (toil.test.batchSystems.batchSystemTest.Job method) (toil.test.jobStores.jobStoreTest.Job method) (toil.test.lib.dockerTest.Job method) (toil.test.mesos.helloWorld.Job method) (toil.test.mesos.stress.Job method) (toil.test.provisioners.restartScript.Job method) (toil.test.sort.restart_sort.Job method) (toil.test.sort.sort.Job method) (toil.test.sort.sortTest.Job method) (toil.test.src.busTest.Job method) (toil.test.src.checkpointTest.Job method) (toil.test.src.deferredFunctionTest.Job method) (toil.test.src.environmentTest.Job method) (toil.test.src.fileStoreTest.Job method) (toil.test.src.helloWorldTest.Job method) (toil.test.src.importExportFileTest.Job method) (toil.test.src.jobDescriptionTest.Job method) (toil.test.src.jobEncapsulationTest.Job method) (toil.test.src.jobFileStoreTest.Job method) (toil.test.src.jobServiceTest.Job method) (toil.test.src.jobTest.Job method) (toil.test.src.promisedRequirementTest.Job method) (toil.test.src.promisesTest.Job method) (toil.test.src.realtimeLoggerTest.Job method) (toil.test.src.restartDAGTest.Job method) (toil.test.src.resumabilityTest.Job method) (toil.test.src.retainTempDirTest.Job method) (toil.test.src.toilContextManagerTest.Job method) (toil.test.src.userDefinedJobArgTypeTest.Job method) (toil.test.utils.utilsTest.Job method) (toil.utils.toilStats.Job method) (toil.wdl.wdltoil.Job method) (toil.worker.Job method) set_from_default_config() (toil.batchSystems.abstractBatchSystem.Config method) (toil.batchSystems.awsBatch.Config method) (toil.batchSystems.cleanup_support.Config method) (toil.batchSystems.kubernetes.Config method) (toil.batchSystems.local_support.Config method) (toil.batchSystems.singleMachine.Config method) (toil.common.Config method) (toil.job.Config method) (toil.jobStores.abstractJobStore.Config method) (toil.leader.Config method) (toil.provisioners.clusterScaler.Config method) (toil.test.batchSystems.batchSystemTest.Config method) (toil.test.batchSystems.test_slurm.Config method) (toil.test.jobStores.jobStoreTest.Config method) (toil.test.provisioners.clusterScalerTest.Config method) (toil.test.src.workerTest.Config method) (toil.test.utils.utilsTest.Config method) (toil.utils.toilDebugFile.Config method) (toil.utils.toilDebugJob.Config method) (toil.utils.toilKill.Config method) (toil.utils.toilStats.Config method) (toil.utils.toilStatus.Config method) (toil.worker.Config method) set_log_level() (in module toil.batchSystems.contained_executor) (in module toil.batchSystems.mesos.executor) (in module toil.realtimeLogger) (in module toil.statsAndLogging) (in module toil.worker) set_logging_from_options() (in module toil.common) (in module toil.job) (in module toil.lib.bioio) (in module toil.statsAndLogging) (in module toil.utils.toilClean) (in module toil.utils.toilConfig) (in module toil.utils.toilDebugFile) (in module toil.utils.toilDebugJob) (in module toil.utils.toilDestroyCluster) (in module toil.utils.toilKill) (in module toil.utils.toilLaunchCluster) (in module toil.utils.toilRsyncCluster) (in module toil.utils.toilServer) (in module toil.utils.toilSshCluster) (in module toil.utils.toilStats) (in module toil.utils.toilStatus) set_message_bus() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method) (toil.batchSystems.abstractBatchSystem.BatchSystemSupport method) (toil.batchSystems.cleanup_support.BatchSystemSupport method) (toil.batchSystems.local_support.BatchSystemSupport method) (toil.batchSystems.mesos.executor.BatchSystemSupport method) (toil.batchSystems.singleMachine.BatchSystemSupport method) (toil.leader.AbstractBatchSystem method) (toil.provisioners.clusterScaler.AbstractBatchSystem method) (toil.test.batchSystems.batch_system_plugin_test.AbstractBatchSystem method) (toil.test.batchSystems.batchSystemTest.AbstractBatchSystem method) (toil.test.batchSystems.batchSystemTest.BatchSystemSupport method) (toil.test.provisioners.clusterScalerTest.AbstractBatchSystem method) set_preemptible() (toil.batchSystems.kubernetes.KubernetesBatchSystem.Placement method) set_root_job() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) set_up_and_run_task() (toil.server.wes.tasks.MultiprocessingTaskRunner static method) (toil.server.wes.toil_backend.MultiprocessingTaskRunner static method) set_up_run() (toil.server.wes.toil_backend.ToilWorkflow method) set_width() (toil.utils.toilStats.ColumnWidths method) setAutoscaledNodeTypes() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method) setEnv() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method) (toil.batchSystems.abstractBatchSystem.BatchSystemSupport method) (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem method) (toil.batchSystems.cleanup_support.BatchSystemSupport method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem method) (toil.batchSystems.local_support.BatchSystemSupport method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem method) (toil.batchSystems.mesos.executor.BatchSystemSupport method) (toil.batchSystems.singleMachine.BatchSystemSupport method) (toil.batchSystems.slurm.AbstractGridEngineBatchSystem method) (toil.batchSystems.torque.AbstractGridEngineBatchSystem method) (toil.leader.AbstractBatchSystem method) (toil.provisioners.clusterScaler.AbstractBatchSystem method) (toil.test.batchSystems.batch_system_plugin_test.AbstractBatchSystem method) (toil.test.batchSystems.batchSystemTest.AbstractBatchSystem method) (toil.test.batchSystems.batchSystemTest.BatchSystemSupport method) (toil.test.provisioners.clusterScalerTest.AbstractBatchSystem method) setLoggingFromOptions() (in module toil.lib.bioio) setNodeCount() (toil.provisioners.clusterScaler.ClusterScaler method) (toil.test.provisioners.clusterScalerTest.ClusterScaler method) setOptions() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem class method) (toil.batchSystems.abstractBatchSystem.Config method) (toil.batchSystems.awsBatch.AWSBatchBatchSystem class method) (toil.batchSystems.awsBatch.Config method) (toil.batchSystems.cleanup_support.Config method) (toil.batchSystems.kubernetes.Config method) (toil.batchSystems.kubernetes.KubernetesBatchSystem class method) (toil.batchSystems.local_support.Config method) (toil.batchSystems.local_support.SingleMachineBatchSystem class method) (toil.batchSystems.mesos.batchSystem.MesosBatchSystem class method) (toil.batchSystems.singleMachine.Config method) (toil.batchSystems.singleMachine.SingleMachineBatchSystem class method) (toil.batchSystems.slurm.SlurmBatchSystem class method) (toil.common.Config method) (toil.job.Config method) (toil.jobStores.abstractJobStore.Config method) (toil.leader.AbstractBatchSystem class method) (toil.leader.Config method) (toil.provisioners.clusterScaler.AbstractBatchSystem class method) (toil.provisioners.clusterScaler.Config method) (toil.test.batchSystems.batch_system_plugin_test.AbstractBatchSystem class method) (toil.test.batchSystems.batch_system_plugin_test.FakeBatchSystem class method) (toil.test.batchSystems.batchSystemTest.AbstractBatchSystem class method) (toil.test.batchSystems.batchSystemTest.Config method) (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystem class method) (toil.test.batchSystems.test_slurm.Config method) (toil.test.jobStores.jobStoreTest.Config method) (toil.test.provisioners.clusterScalerTest.AbstractBatchSystem class method) (toil.test.provisioners.clusterScalerTest.Config method) (toil.test.src.jobServiceTest.SingleMachineBatchSystem class method) (toil.test.src.workerTest.Config method) (toil.test.utils.utilsTest.Config method) (toil.utils.toilDebugFile.Config method) (toil.utils.toilDebugJob.Config method) (toil.utils.toilKill.Config method) (toil.utils.toilStats.Config method) (toil.utils.toilStatus.Config method) (toil.worker.Config method) setRootJob() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) 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setupJobAfterFailure() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) 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toil.provisioners.aws.awsProvisioner) (class in toil.provisioners.clusterScaler) (class in toil.provisioners.gceProvisioner) (class in toil.test.provisioners.clusterScalerTest) shapes() (toil.provisioners.clusterScaler.NodeReservation method) (toil.test.provisioners.clusterScalerTest.NodeReservation method) share_files() (toil.wdl.wdltoil.ToilWDLStdLibBase method) sharedFileNameRegex (toil.cwl.cwltoil.AbstractJobStore attribute) (toil.cwl.utils.AbstractJobStore attribute) (toil.fileStores.abstractFileStore.AbstractJobStore attribute) (toil.fileStores.cachingFileStore.AbstractJobStore attribute) (toil.fileStores.nonCachingFileStore.AbstractJobStore attribute) (toil.jobStores.abstractJobStore.AbstractJobStore attribute) (toil.jobStores.aws.jobStore.AbstractJobStore attribute) (toil.jobStores.fileJobStore.AbstractJobStore attribute) (toil.jobStores.googleJobStore.AbstractJobStore attribute) (toil.leader.AbstractJobStore attribute) (toil.serviceManager.AbstractJobStore attribute) (toil.toilState.AbstractJobStore attribute) (toil.utils.toilStats.AbstractJobStore attribute) (toil.wdl.wdltoil.AbstractJobStore attribute) (toil.worker.AbstractJobStore attribute) sharedFileOwnerID (toil.jobStores.aws.jobStore.AWSJobStore attribute) (toil.test.lib.aws.test_s3.AWSJobStore attribute) shutdown() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method) (toil.batchSystems.abstractBatchSystem.AbstractFileStore class method) (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem method) (toil.batchSystems.awsBatch.AWSBatchBatchSystem method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem method) (toil.batchSystems.kubernetes.KubernetesBatchSystem method) (toil.batchSystems.local_support.SingleMachineBatchSystem method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem method) (toil.batchSystems.mesos.batchSystem.MesosBatchSystem method) 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shutDown() (toil.provisioners.clusterScaler.ClusterScaler method) shutdown() (toil.provisioners.clusterScaler.ScalerThread method) (toil.serviceManager.ServiceManager method) (toil.statsAndLogging.StatsAndLogging method) (toil.test.batchSystems.batch_system_plugin_test.AbstractBatchSystem method) (toil.test.batchSystems.batch_system_plugin_test.FakeBatchSystem method) (toil.test.batchSystems.batchSystemTest.AbstractBatchSystem method) (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystem method) (toil.test.cwl.cwlTest.AbstractFileStore class method) (toil.test.jobStores.jobStoreTest.StatsAndLogging method) (toil.test.provisioners.clusterScalerTest.AbstractBatchSystem method) shutDown() (toil.test.provisioners.clusterScalerTest.ClusterScaler method) (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method) shutdown() (toil.test.provisioners.clusterScalerTest.ScalerThread method) (toil.test.src.jobServiceTest.SingleMachineBatchSystem method) 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(toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem method) (toil.batchSystems.slurm.AbstractGridEngineBatchSystem method) (toil.batchSystems.torque.AbstractGridEngineBatchSystem method) sleepTime (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemJobTest attribute) slow() (in module toil.test) (in module toil.test.batchSystems.batchSystemTest) (in module toil.test.cwl.cwlTest) (in module toil.test.jobStores.jobStoreTest) (in module toil.test.lib.dockerTest) (in module toil.test.provisioners.aws.awsProvisionerTest) (in module toil.test.provisioners.clusterScalerTest) (in module toil.test.provisioners.clusterTest) (in module toil.test.provisioners.gceProvisionerTest) (in module toil.test.sort.sortTest) (in module toil.test.src.autoDeploymentTest) (in module toil.test.src.checkpointTest) (in module toil.test.src.deferredFunctionTest) (in module toil.test.src.environmentTest) (in module toil.test.src.fileStoreTest) (in module toil.test.src.importExportFileTest) (in module toil.test.src.jobFileStoreTest) (in module toil.test.src.jobServiceTest) (in module toil.test.src.jobTest) (in module toil.test.src.miscTests) (in module toil.test.src.promisedRequirementTest) (in module toil.test.src.regularLogTest) (in module toil.test.src.restartDAGTest) (in module toil.test.src.resumabilityTest) (in module toil.test.src.toilContextManagerTest) (in module toil.test.src.userDefinedJobArgTypeTest) (in module toil.test.utils.toilDebugTest) (in module toil.test.utils.utilsTest) (in module toil.test.wdl.wdltoil_test) (in module toil.test.wdl.wdltoil_test_kubernetes) slow_down() (in module toil.batchSystems.awsBatch) (in module toil.batchSystems.kubernetes) (in module toil.lib.misc) slurm_batch_system_factory() (in module toil.batchSystems.registry) SlurmBatchSystem (class in toil.batchSystems.slurm) SlurmBatchSystem.GridEngineThread (class in toil.batchSystems.slurm) SlurmBatchSystemTest (class in toil.test.batchSystems.batchSystemTest) SlurmTest (class in toil.test.batchSystems.test_slurm) smoothEstimate() (toil.provisioners.clusterScaler.ClusterScaler method) (toil.test.provisioners.clusterScalerTest.ClusterScaler method) sort() (in module toil.test.sort.restart_sort) (in module toil.test.sort.sort) (in module toil.test.sort.sortTest) sort_category_choices (in module toil.utils.toilStats) sort_field_choices (in module toil.utils.toilStats) sort_jobs() (in module toil.utils.toilStats) sort_options() (toil.server.wes.tasks.ToilWorkflowRunner method) sortMemory (in module toil.test.sort.restart_sort) (in module toil.test.sort.sort) SortTest (class in toil.test.sort.sortTest) SOURCE_IMAGE (toil.provisioners.gceProvisioner.GCEProvisioner attribute) SPACE_CATEGORIES (in module toil.utils.toilStats) split() (in module toil.provisioners.clusterScaler) sprint_tag() (in module toil.utils.toilStats) SQLITE_TIMEOUT_SECS (in module toil.fileStores.cachingFileStore) sseKey (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) sseKeyPath (toil.jobStores.aws.jobStore.AWSJobStore property) (toil.test.lib.aws.test_s3.AWSJobStore property) sshAppliance() (toil.provisioners.abstractProvisioner.Node method) (toil.provisioners.aws.awsProvisioner.Node method) (toil.provisioners.gceProvisioner.Node method) (toil.provisioners.node.Node method) (toil.test.provisioners.clusterScalerTest.Node method) sshInstance() (toil.provisioners.abstractProvisioner.Node method) (toil.provisioners.aws.awsProvisioner.Node method) (toil.provisioners.gceProvisioner.Node method) (toil.provisioners.node.Node method) (toil.test.provisioners.clusterScalerTest.Node method) sshUtil() (toil.test.cactus.test_cactus_integration.AbstractClusterTest method) (toil.test.provisioners.aws.awsProvisionerTest.AbstractClusterTest method) (toil.test.provisioners.clusterTest.AbstractClusterTest method) (toil.test.provisioners.gceProvisionerTest.AbstractGCEAutoscaleTest method) (toil.test.wdl.wdltoil_test_kubernetes.AbstractClusterTest method) start() (toil.batchSystems.abstractBatchSystem.Toil method) (toil.batchSystems.awsBatch.Toil method) (toil.batchSystems.cleanup_support.Toil method) (toil.batchSystems.kubernetes.Toil method) (toil.batchSystems.singleMachine.Toil method) (toil.common.Toil method) (toil.cwl.cwltoil.Job.Service method) (toil.cwl.cwltoil.Toil method) (toil.exceptions.StatsAndLogging method) (toil.fileStores.abstractFileStore.Job.Service method) (toil.fileStores.abstractFileStore.Toil method) (toil.fileStores.cachingFileStore.Job.Service method) (toil.fileStores.nonCachingFileStore.Job.Service method) (toil.job.Job.Service method) (toil.job.Toil method) (toil.jobStores.aws.jobStore.Job.Service method) (toil.leader.ServiceManager method) (toil.leader.StatsAndLogging method) (toil.server.wes.tasks.Toil method) (toil.serviceManager.ServiceManager method) (toil.statsAndLogging.StatsAndLogging method) (toil.test.batchSystems.batch_system_plugin_test.Toil method) (toil.test.batchSystems.batchSystemTest.Job.Service method) (toil.test.batchSystems.batchSystemTest.Service method) (toil.test.batchSystems.batchSystemTest.Toil method) (toil.test.jobStores.jobStoreTest.Job.Service method) (toil.test.jobStores.jobStoreTest.StatsAndLogging method) (toil.test.jobStores.jobStoreTest.Toil method) (toil.test.lib.dockerTest.Job.Service method) (toil.test.lib.dockerTest.Toil method) (toil.test.mesos.helloWorld.Job.Service method) (toil.test.mesos.helloWorld.Toil method) (toil.test.mesos.stress.Job.Service method) (toil.test.options.options.Toil method) (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method) (toil.test.provisioners.restartScript.Job.Service method) (toil.test.sort.restart_sort.Job.Service method) (toil.test.sort.restart_sort.Toil method) (toil.test.sort.sort.Job.Service method) (toil.test.sort.sort.Toil method) (toil.test.sort.sortTest.Job.Service method) (toil.test.sort.sortTest.Toil method) (toil.test.src.busTest.Job.Service method) (toil.test.src.busTest.Toil method) (toil.test.src.checkpointTest.Job.Service method) (toil.test.src.deferredFunctionTest.Job.Service method) (toil.test.src.environmentTest.Job.Service method) (toil.test.src.environmentTest.Toil method) (toil.test.src.fileStoreTest.Job.Service method) (toil.test.src.fileStoreTest.Toil method) (toil.test.src.helloWorldTest.Job.Service method) (toil.test.src.importExportFileTest.Job.Service method) (toil.test.src.importExportFileTest.Toil method) (toil.test.src.jobDescriptionTest.Job.Service method) (toil.test.src.jobDescriptionTest.Toil method) (toil.test.src.jobEncapsulationTest.Job.Service method) (toil.test.src.jobFileStoreTest.Job.Service method) (toil.test.src.jobFileStoreTest.Toil method) (toil.test.src.jobServiceTest.Job.Service method) (toil.test.src.jobServiceTest.ToySerializableService method) (toil.test.src.jobServiceTest.ToyService method) (toil.test.src.jobTest.Job.Service method) (toil.test.src.jobTest.Toil method) (toil.test.src.jobTest.TrivialService method) (toil.test.src.promisedRequirementTest.Job.Service method) (toil.test.src.promisesTest.Job.Service method) (toil.test.src.realtimeLoggerTest.Job.Service method) (toil.test.src.restartDAGTest.Job.Service method) (toil.test.src.restartDAGTest.Toil method) (toil.test.src.resumabilityTest.Job.Service method) (toil.test.src.retainTempDirTest.Job.Service method) (toil.test.src.toilContextManagerTest.Job.Service method) (toil.test.src.toilContextManagerTest.Toil method) (toil.test.src.userDefinedJobArgTypeTest.Job.Service method) (toil.test.utils.toilKillTest.Toil method) (toil.test.utils.utilsTest.Job.Service method) (toil.test.utils.utilsTest.Toil method) (toil.utils.toilClean.Toil method) (toil.utils.toilDebugFile.Toil method) (toil.utils.toilDebugJob.Toil method) (toil.utils.toilKill.Toil method) (toil.utils.toilStats.Job.Service method) (toil.utils.toilStats.Toil method) (toil.utils.toilStatus.StatsAndLogging method) (toil.utils.toilStatus.Toil method) (toil.wdl.wdltoil.Job.Service method) (toil.wdl.wdltoil.Toil method) (toil.worker.Job.Service method) (toil.worker.Toil method) start_server() (in module toil.server.app) startCommit() (toil.batchSystems.abstractBatchSystem.AbstractFileStore method) (toil.cwl.cwltoil.AbstractFileStore method) (toil.cwl.utils.AbstractFileStore method) (toil.fileStores.abstractFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.CachingFileStore method) (toil.fileStores.nonCachingFileStore.AbstractFileStore method) (toil.fileStores.nonCachingFileStore.NonCachingFileStore method) (toil.test.cwl.cwlTest.AbstractFileStore method) (toil.wdl.wdltoil.AbstractFileStore method) (toil.worker.AbstractFileStore method) startCommitThread() (toil.fileStores.cachingFileStore.CachingFileStore method) startDashboard() (toil.common.ToilMetrics method) (toil.leader.ToilMetrics method) startStats() (toil.provisioners.clusterScaler.ClusterStats method) startToil() (toil.cwl.cwltoil.Job.Runner static method) (toil.fileStores.abstractFileStore.Job.Runner static method) (toil.fileStores.cachingFileStore.Job.Runner static method) (toil.fileStores.nonCachingFileStore.Job.Runner static method) (toil.job.Job.Runner static method) (toil.jobStores.aws.jobStore.Job.Runner static method) (toil.test.batchSystems.batchSystemTest.Job.Runner static method) (toil.test.jobStores.jobStoreTest.Job.Runner static method) (toil.test.lib.dockerTest.Job.Runner static method) (toil.test.mesos.helloWorld.Job.Runner static method) (toil.test.mesos.stress.Job.Runner static method) (toil.test.provisioners.restartScript.Job.Runner static method) (toil.test.sort.restart_sort.Job.Runner static method) (toil.test.sort.sort.Job.Runner static method) (toil.test.sort.sortTest.Job.Runner static method) (toil.test.src.busTest.Job.Runner static method) (toil.test.src.checkpointTest.Job.Runner static method) (toil.test.src.deferredFunctionTest.Job.Runner static method) (toil.test.src.environmentTest.Job.Runner static method) (toil.test.src.fileStoreTest.Job.Runner static method) (toil.test.src.helloWorldTest.Job.Runner static method) (toil.test.src.importExportFileTest.Job.Runner static method) (toil.test.src.jobDescriptionTest.Job.Runner static method) (toil.test.src.jobEncapsulationTest.Job.Runner static method) (toil.test.src.jobFileStoreTest.Job.Runner static method) (toil.test.src.jobServiceTest.Job.Runner static method) (toil.test.src.jobTest.Job.Runner static method) (toil.test.src.promisedRequirementTest.Job.Runner static method) (toil.test.src.promisesTest.Job.Runner static method) (toil.test.src.realtimeLoggerTest.Job.Runner static method) (toil.test.src.restartDAGTest.Job.Runner static method) (toil.test.src.resumabilityTest.Job.Runner static method) (toil.test.src.retainTempDirTest.Job.Runner static method) (toil.test.src.toilContextManagerTest.Job.Runner static method) (toil.test.src.userDefinedJobArgTypeTest.Job.Runner static method) (toil.test.utils.utilsTest.Job.Runner static method) (toil.utils.toilStats.Job.Runner static method) (toil.wdl.wdltoil.Job.Runner static method) (toil.worker.Job.Runner static method) STATE_DIR_STEM (toil.batchSystems.abstractBatchSystem.DeferredFunctionManager attribute) (toil.deferred.DeferredFunctionManager attribute) (toil.worker.DeferredFunctionManager attribute) state_polling_timeout (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) state_store_cache (in module toil.server.utils) STATE_TO_EXIT_REASON (in module toil.batchSystems.awsBatch) statePollingWait (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) stats (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) stats_name (toil.bus.Names attribute) (toil.job.Names attribute) StatsAndLogging (class in toil.exceptions) (class in toil.leader) (class in toil.statsAndLogging) (class in toil.test.jobStores.jobStoreTest) (class in toil.utils.toilStatus) statsAndLoggingAggregator() (toil.exceptions.StatsAndLogging class method) (toil.leader.StatsAndLogging class method) (toil.statsAndLogging.StatsAndLogging class method) (toil.test.jobStores.jobStoreTest.StatsAndLogging class method) (toil.utils.toilStatus.StatsAndLogging class method) statsCommand (toil.test.utils.utilsTest.UtilsTest property) StatsDict (class in toil.worker) statsFileOwnerID (toil.jobStores.aws.jobStore.AWSJobStore attribute) (toil.test.lib.aws.test_s3.AWSJobStore attribute) statusCommand() (toil.test.utils.utilsTest.UtilsTest method) statusUpdate() (toil.batchSystems.mesos.batchSystem.MesosBatchSystem method) statusWait (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) stderr_used() (toil.wdl.wdltoil.ToilWDLStdLibTaskOutputs method) stdout_used() (toil.wdl.wdltoil.ToilWDLStdLibTaskOutputs method) StepValueFrom (class in toil.cwl.cwltoil) STOP (in module toil.lib.docker) (in module toil.test.lib.dockerTest) stop() (toil.cwl.cwltoil.Job.Service method) (toil.fileStores.abstractFileStore.Job.Service method) (toil.fileStores.cachingFileStore.Job.Service method) (toil.fileStores.nonCachingFileStore.Job.Service method) (toil.job.Job.Service method) (toil.jobStores.aws.jobStore.Job.Service method) (toil.test.batchSystems.batchSystemTest.Job.Service method) (toil.test.batchSystems.batchSystemTest.Service method) (toil.test.jobStores.jobStoreTest.Job.Service method) (toil.test.lib.dockerTest.Job.Service method) (toil.test.mesos.helloWorld.Job.Service method) (toil.test.mesos.stress.Job.Service method) (toil.test.provisioners.restartScript.Job.Service method) (toil.test.sort.restart_sort.Job.Service method) (toil.test.sort.sort.Job.Service method) (toil.test.sort.sortTest.Job.Service method) (toil.test.src.busTest.Job.Service method) (toil.test.src.checkpointTest.Job.Service method) (toil.test.src.deferredFunctionTest.Job.Service method) (toil.test.src.environmentTest.Job.Service method) (toil.test.src.fileStoreTest.Job.Service method) (toil.test.src.helloWorldTest.Job.Service method) (toil.test.src.importExportFileTest.Job.Service method) (toil.test.src.jobDescriptionTest.Job.Service method) (toil.test.src.jobEncapsulationTest.Job.Service method) (toil.test.src.jobFileStoreTest.Job.Service method) (toil.test.src.jobServiceTest.Job.Service method) (toil.test.src.jobServiceTest.ToySerializableService method) (toil.test.src.jobServiceTest.ToyService method) (toil.test.src.jobTest.Job.Service method) (toil.test.src.jobTest.TrivialService method) (toil.test.src.promisedRequirementTest.Job.Service method) (toil.test.src.promisesTest.Job.Service method) (toil.test.src.realtimeLoggerTest.Job.Service method) (toil.test.src.restartDAGTest.Job.Service method) (toil.test.src.resumabilityTest.Job.Service method) (toil.test.src.retainTempDirTest.Job.Service method) (toil.test.src.toilContextManagerTest.Job.Service method) (toil.test.src.userDefinedJobArgTypeTest.Job.Service method) (toil.test.utils.utilsTest.Job.Service method) (toil.utils.toilStats.Job.Service method) (toil.wdl.wdltoil.Job.Service method) (toil.worker.Job.Service method) streamingFileStoreString (in module toil.test.src.jobFileStoreTest) strict_bool() (in module toil.batchSystems.mesos.batchSystem) (in module toil.jobStores.aws.jobStore) (in module toil.lib.memoize) (in module toil.resource) strtobool() (in module toil.lib.conversions) (in module toil.options.common) (in module toil.statsAndLogging) (in module toil.utils.toilDebugFile) (in module toil.wdl.wdltoil) StubHttpRequestHandler (class in toil.test.jobStores.jobStoreTest) submit_run() (in module toil.server.cli.wes_cwl_runner) submitJob() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.gridengine.GridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.htcondor.HTCondorBatchSystem.GridEngineThread method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.lsf.LSFBatchSystem.GridEngineThread method) (toil.batchSystems.slurm.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.slurm.SlurmBatchSystem.GridEngineThread method) (toil.batchSystems.torque.AbstractGridEngineBatchSystem.GridEngineThread method) (toil.batchSystems.torque.TorqueBatchSystem.GridEngineThread method) subprocessDockerCall() (in module toil.lib.docker) subscribe() (toil.batchSystems.abstractBatchSystem.MessageBus method) (toil.bus.MessageBus method) (toil.common.MessageBus method) (toil.test.src.busTest.MessageBus method) (toil.toilState.MessageBus method) subtract() (toil.provisioners.clusterScaler.NodeReservation method) (toil.test.provisioners.clusterScalerTest.NodeReservation method) successor_returned() (toil.leader.ToilState method) (toil.serviceManager.ToilState method) (toil.toilState.ToilState method) successors_by_phase() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) successors_pending() (toil.leader.ToilState method) (toil.serviceManager.ToilState method) (toil.toilState.ToilState method) successorsAndServiceHosts() (toil.batchSystems.abstractBatchSystem.JobDescription method) (toil.batchSystems.awsBatch.JobDescription method) (toil.batchSystems.kubernetes.JobDescription method) (toil.batchSystems.local_support.JobDescription method) (toil.batchSystems.mesos.batchSystem.JobDescription method) (toil.batchSystems.singleMachine.JobDescription method) (toil.fileStores.abstractFileStore.JobDescription method) (toil.fileStores.cachingFileStore.JobDescription method) (toil.fileStores.nonCachingFileStore.JobDescription method) (toil.job.JobDescription method) (toil.jobStores.abstractJobStore.JobDescription method) (toil.jobStores.aws.jobStore.JobDescription method) (toil.leader.JobDescription method) (toil.provisioners.clusterScaler.JobDescription method) (toil.test.batchSystems.batch_system_plugin_test.JobDescription method) (toil.test.batchSystems.batchSystemTest.JobDescription method) (toil.test.jobStores.jobStoreTest.JobDescription method) (toil.test.provisioners.clusterScalerTest.JobDescription method) (toil.test.src.jobDescriptionTest.JobDescription method) (toil.test.src.workerTest.JobDescription method) (toil.toilState.JobDescription method) (toil.utils.toilStatus.JobDescription method) (toil.worker.JobDescription method) SUPPORTED_HTTP_ERRORS (in module toil.lib.retry) supportedClusterTypes() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AWSProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.provisioners.gceProvisioner.GCEProvisioner method) (toil.test.provisioners.aws.awsProvisionerTest.AWSProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method) supportsAutoDeployment() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem class method) (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem class method) (toil.batchSystems.awsBatch.AWSBatchBatchSystem class method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem class method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem class method) (toil.batchSystems.kubernetes.KubernetesBatchSystem class method) (toil.batchSystems.local_support.SingleMachineBatchSystem class method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem class method) (toil.batchSystems.mesos.batchSystem.MesosBatchSystem class method) (toil.batchSystems.singleMachine.SingleMachineBatchSystem class method) (toil.batchSystems.slurm.AbstractGridEngineBatchSystem class method) (toil.batchSystems.torque.AbstractGridEngineBatchSystem class method) (toil.leader.AbstractBatchSystem class method) (toil.provisioners.clusterScaler.AbstractBatchSystem class method) (toil.test.batchSystems.batch_system_plugin_test.AbstractBatchSystem class method) (toil.test.batchSystems.batch_system_plugin_test.FakeBatchSystem class method) (toil.test.batchSystems.batchSystemTest.AbstractBatchSystem class method) (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystem class method) (toil.test.provisioners.clusterScalerTest.AbstractBatchSystem class method) (toil.test.src.jobServiceTest.SingleMachineBatchSystem class method) supportsWallTime() (toil.test.batchSystems.batchSystemTest.AWSBatchBatchSystemTest method) (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemTest method) (toil.test.batchSystems.batchSystemTest.KubernetesBatchSystemTest method) (toil.test.batchSystems.batchSystemTest.MesosBatchSystemTest method) (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystemTest method) supportsWorkerCleanup() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem class method) (toil.batchSystems.abstractGridEngineBatchSystem.BatchSystemCleanupSupport class method) (toil.batchSystems.awsBatch.BatchSystemCleanupSupport class method) (toil.batchSystems.cleanup_support.BatchSystemCleanupSupport class method) (toil.batchSystems.kubernetes.BatchSystemCleanupSupport class method) (toil.batchSystems.local_support.SingleMachineBatchSystem class method) (toil.batchSystems.mesos.batchSystem.MesosBatchSystem class method) (toil.batchSystems.singleMachine.SingleMachineBatchSystem class method) (toil.leader.AbstractBatchSystem class method) (toil.provisioners.clusterScaler.AbstractBatchSystem class method) (toil.test.batchSystems.batch_system_plugin_test.AbstractBatchSystem class method) (toil.test.batchSystems.batch_system_plugin_test.BatchSystemCleanupSupport class method) (toil.test.batchSystems.batchSystemTest.AbstractBatchSystem class method) (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystem class method) (toil.test.provisioners.clusterScalerTest.AbstractBatchSystem class method) (toil.test.src.jobServiceTest.SingleMachineBatchSystem class method) suppress_exotic_logging() (in module toil.statsAndLogging) symlinkImports (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) sync_memoize() (in module toil.lib.memoize) (in module toil.lib.objects) SYS_MAX_SIZE (in module toil.batchSystems.kubernetes) (in module toil.batchSystems.singleMachine) (in module toil.options.common) (in module toil.utils.toilStats) system() (in module toil.lib.bioio) (in module toil.test.utils.utilsTest) SystemTest (class in toil.test.src.systemTest)

T

T (in module toil.job) t2_micro (in module toil.test.provisioners.clusterScalerTest) TagGenerationTest (class in toil.test.lib.aws.test_utils) targetTime (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) task_filter() (in module toil.server.wes.amazon_wes_utils) TaskData (in module toil.batchSystems.mesos) (in module toil.batchSystems.mesos.batchSystem) TaskLog (in module toil.server.wes.abstract_backend) (in module toil.server.wes.amazon_wes_utils) (in module toil.server.wes.toil_backend) TaskRunner (class in toil.server.wes.tasks) (class in toil.server.wes.toil_backend) tearDown() (toil.test.batchSystems.batch_system_plugin_test.ToilTest method) (toil.test.batchSystems.batchSystemTest.BatchSystemPluginTest method) (toil.test.batchSystems.batchSystemTest.GridEngineBatchSystemTest method) (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemJobTest method) (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemTest method) (toil.test.batchSystems.batchSystemTest.HTCondorBatchSystemTest method) (toil.test.batchSystems.batchSystemTest.MaxCoresSingleMachineBatchSystemTest method) (toil.test.batchSystems.batchSystemTest.MesosBatchSystemJobTest method) (toil.test.batchSystems.batchSystemTest.MesosBatchSystemTest method) (toil.test.batchSystems.batchSystemTest.SlurmBatchSystemTest method) (toil.test.batchSystems.batchSystemTest.ToilTest method) (toil.test.batchSystems.batchSystemTest.TorqueBatchSystemTest method) (toil.test.batchSystems.test_lsf_helper.ToilTest method) (toil.test.batchSystems.test_slurm.ToilTest method) (toil.test.cactus.test_cactus_integration.AbstractClusterTest method) (toil.test.cwl.cwlTest.CWLv10Test method) (toil.test.cwl.cwlTest.CWLv11Test method) (toil.test.cwl.cwlTest.CWLv12Test method) (toil.test.cwl.cwlTest.CWLWorkflowTest method) (toil.test.cwl.cwlTest.ToilTest method) (toil.test.docs.scriptsTest.ToilDocumentationTest method) (toil.test.docs.scriptsTest.ToilTest method) (toil.test.jobStores.jobStoreTest.AbstractEncryptedJobStoreTest.Test method) (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) (toil.test.jobStores.jobStoreTest.ToilTest method) (toil.test.lib.aws.test_iam.ToilTest method) (toil.test.lib.aws.test_s3.ToilTest method) (toil.test.lib.aws.test_utils.ToilTest method) (toil.test.lib.dockerTest.ToilTest method) (toil.test.lib.test_conversions.ToilTest method) (toil.test.lib.test_ec2.ToilTest method) (toil.test.lib.test_misc.ToilTest method) (toil.test.lib.test_misc.UserNameUnvailableTest method) (toil.test.lib.test_misc.UserNameVeryBrokenTest method) (toil.test.mesos.MesosDataStructuresTest.ToilTest method) (toil.test.options.options.ToilTest method) (toil.test.provisioners.aws.awsProvisionerTest.AbstractClusterTest method) (toil.test.provisioners.aws.awsProvisionerTest.ToilTest method) (toil.test.provisioners.clusterScalerTest.ToilTest method) (toil.test.provisioners.clusterTest.AbstractClusterTest method) (toil.test.provisioners.clusterTest.ToilTest method) (toil.test.provisioners.gceProvisionerTest.AbstractGCEAutoscaleTest method) (toil.test.provisioners.gceProvisionerTest.ToilTest method) (toil.test.provisioners.provisionerTest.ToilTest method) (toil.test.server.serverTest.AbstractToilWESServerTest method) (toil.test.server.serverTest.ToilTest method) (toil.test.sort.sortTest.SortTest method) (toil.test.sort.sortTest.ToilTest method) (toil.test.src.busTest.ToilTest method) (toil.test.src.checkpointTest.ToilTest method) (toil.test.src.deferredFunctionTest.ToilTest method) (toil.test.src.dockerCheckTest.ToilTest method) (toil.test.src.environmentTest.ToilTest method) (toil.test.src.fileStoreTest.ToilTest method) (toil.test.src.helloWorldTest.ToilTest method) (toil.test.src.importExportFileTest.ToilTest method) (toil.test.src.jobDescriptionTest.JobDescriptionTest method) (toil.test.src.jobDescriptionTest.ToilTest method) (toil.test.src.jobEncapsulationTest.ToilTest method) (toil.test.src.jobFileStoreTest.ToilTest method) (toil.test.src.jobServiceTest.ToilTest method) (toil.test.src.jobTest.ToilTest method) (toil.test.src.miscTests.ToilTest method) (toil.test.src.promisedRequirementTest.MesosPromisedRequirementsTest method) (toil.test.src.promisedRequirementTest.SingleMachinePromisedRequirementsTest method) (toil.test.src.promisesTest.ToilTest method) (toil.test.src.realtimeLoggerTest.ToilTest method) (toil.test.src.regularLogTest.ToilTest method) (toil.test.src.resourceTest.ToilTest method) (toil.test.src.restartDAGTest.RestartDAGTest method) (toil.test.src.restartDAGTest.ToilTest method) (toil.test.src.resumabilityTest.ToilTest method) (toil.test.src.retainTempDirTest.CleanWorkDirTest method) (toil.test.src.retainTempDirTest.ToilTest method) (toil.test.src.systemTest.ToilTest method) (toil.test.src.threadingTest.ToilTest method) (toil.test.src.toilContextManagerTest.ToilContextManagerTest method) (toil.test.src.toilContextManagerTest.ToilTest method) (toil.test.src.userDefinedJobArgTypeTest.ToilTest method) (toil.test.src.workerTest.ToilTest method) (toil.test.ToilTest method) (toil.test.utils.toilDebugTest.ToilTest method) (toil.test.utils.toilKillTest.ToilKillTest method) (toil.test.utils.toilKillTest.ToilTest method) (toil.test.utils.utilsTest.ToilTest method) (toil.test.utils.utilsTest.UtilsTest method) (toil.test.wdl.wdltoil_test.BaseWDLTest method) (toil.test.wdl.wdltoil_test.ToilTest method) (toil.test.wdl.wdltoil_test_kubernetes.AbstractClusterTest method) tearDownClass() (toil.test.batchSystems.batch_system_plugin_test.ToilTest class method) (toil.test.batchSystems.batchSystemTest.ToilTest class method) (toil.test.batchSystems.test_lsf_helper.ToilTest class method) (toil.test.batchSystems.test_slurm.ToilTest class method) (toil.test.cwl.cwlTest.ToilTest class method) (toil.test.docs.scriptsTest.ToilTest class method) (toil.test.jobStores.jobStoreTest.ToilTest class method) (toil.test.lib.aws.test_iam.ToilTest class method) (toil.test.lib.aws.test_s3.S3Test class method) (toil.test.lib.aws.test_s3.ToilTest class method) (toil.test.lib.aws.test_utils.ToilTest class method) (toil.test.lib.dockerTest.ToilTest class method) (toil.test.lib.test_conversions.ToilTest class method) (toil.test.lib.test_ec2.ToilTest class method) (toil.test.lib.test_misc.ToilTest class method) (toil.test.mesos.MesosDataStructuresTest.ToilTest class method) (toil.test.options.options.ToilTest class method) (toil.test.provisioners.aws.awsProvisionerTest.ToilTest class method) (toil.test.provisioners.clusterScalerTest.ToilTest class method) (toil.test.provisioners.clusterTest.ToilTest class method) (toil.test.provisioners.gceProvisionerTest.ToilTest class method) (toil.test.provisioners.provisionerTest.ToilTest class method) (toil.test.server.serverTest.BucketUsingTest class method) (toil.test.server.serverTest.ToilTest class method) (toil.test.sort.sortTest.ToilTest class method) (toil.test.src.busTest.ToilTest class method) (toil.test.src.checkpointTest.ToilTest class method) (toil.test.src.deferredFunctionTest.ToilTest class method) (toil.test.src.dockerCheckTest.ToilTest class method) (toil.test.src.environmentTest.ToilTest class method) (toil.test.src.fileStoreTest.ToilTest class method) (toil.test.src.helloWorldTest.ToilTest class method) (toil.test.src.importExportFileTest.ToilTest class method) (toil.test.src.jobDescriptionTest.ToilTest class method) (toil.test.src.jobEncapsulationTest.ToilTest class method) (toil.test.src.jobFileStoreTest.ToilTest class method) (toil.test.src.jobServiceTest.ToilTest class method) (toil.test.src.jobTest.ToilTest class method) (toil.test.src.miscTests.ToilTest class method) (toil.test.src.promisesTest.ToilTest class method) (toil.test.src.realtimeLoggerTest.ToilTest class method) (toil.test.src.regularLogTest.ToilTest class method) (toil.test.src.resourceTest.ToilTest class method) (toil.test.src.restartDAGTest.ToilTest class method) (toil.test.src.resumabilityTest.ToilTest class method) (toil.test.src.retainTempDirTest.ToilTest class method) (toil.test.src.systemTest.ToilTest class method) (toil.test.src.threadingTest.ToilTest class method) (toil.test.src.toilContextManagerTest.ToilTest class method) (toil.test.src.userDefinedJobArgTypeTest.ToilTest class method) (toil.test.src.workerTest.ToilTest class method) (toil.test.ToilTest class method) (toil.test.utils.toilDebugTest.ToilTest class method) (toil.test.utils.toilKillTest.ToilTest class method) (toil.test.utils.utilsTest.ToilTest class method) (toil.test.wdl.wdltoil_test.ToilTest class method) (toil.test.wdl.wdltoil_test.WDLConformanceTests class method) tearDownModule() (in module toil.test.jobStores.jobStoreTest) tempDir (toil.cwl.cwltoil.Job property) (toil.fileStores.abstractFileStore.Job property) (toil.fileStores.cachingFileStore.Job property) (toil.fileStores.nonCachingFileStore.Job property) (toil.job.Job property) (toil.jobStores.aws.jobStore.Job property) (toil.test.batchSystems.batchSystemTest.Job property) (toil.test.jobStores.jobStoreTest.Job property) (toil.test.lib.dockerTest.Job property) (toil.test.mesos.helloWorld.Job property) (toil.test.mesos.stress.Job property) (toil.test.provisioners.restartScript.Job property) (toil.test.sort.restart_sort.Job property) (toil.test.sort.sort.Job property) (toil.test.sort.sortTest.Job property) (toil.test.src.busTest.Job property) (toil.test.src.checkpointTest.Job property) (toil.test.src.deferredFunctionTest.Job property) (toil.test.src.environmentTest.Job property) (toil.test.src.fileStoreTest.Job property) (toil.test.src.helloWorldTest.Job property) (toil.test.src.importExportFileTest.Job property) (toil.test.src.jobDescriptionTest.Job property) (toil.test.src.jobEncapsulationTest.Job property) (toil.test.src.jobFileStoreTest.Job property) (toil.test.src.jobServiceTest.Job property) (toil.test.src.jobTest.Job property) (toil.test.src.promisedRequirementTest.Job property) (toil.test.src.promisesTest.Job property) (toil.test.src.realtimeLoggerTest.Job property) (toil.test.src.restartDAGTest.Job property) (toil.test.src.resumabilityTest.Job property) (toil.test.src.retainTempDirTest.Job property) (toil.test.src.toilContextManagerTest.Job property) (toil.test.src.userDefinedJobArgTypeTest.Job property) (toil.test.utils.utilsTest.Job property) (toil.utils.toilStats.Job property) (toil.wdl.wdltoil.Job property) (toil.worker.Job property) tempFileContaining() (in module toil.test.src.resourceTest) tempFileTestErrorJob() (in module toil.test.src.retainTempDirTest) tempFileTestJob() (in module toil.test.src.retainTempDirTest) TemporaryID (class in toil.job) (class in toil.jobStores.fileJobStore) (class in toil.leader) (class in toil.test.jobStores.jobStoreTest) (class in toil.test.src.jobDescriptionTest) (class in toil.wdl.wdltoil) TERMINAL_STATES (in module toil.batchSystems.slurm) (in module toil.server.utils) terminateNodes() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AWSProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.provisioners.gceProvisioner.GCEProvisioner method) (toil.test.provisioners.aws.awsProvisionerTest.AWSProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method) tes_bearer_token (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) tes_endpoint (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) tes_password (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) tes_user (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) test() (toil.test.batchSystems.batchSystemTest.MaxCoresSingleMachineBatchSystemTest method) (toil.test.provisioners.aws.awsProvisionerTest.PreemptibleDeficitCompensationTest method) (toil.test.src.promisesTest.CachedUnpicklingJobStoreTest method) (toil.test.src.promisesTest.ChainedIndexedPromisesTest method) (toil.test.src.promisesTest.PathIndexingPromiseTest method) (toil.test.src.resumabilityTest.ResumabilityTest method) test_add_batch_system_factory() (toil.test.batchSystems.batchSystemTest.BatchSystemPluginTest method) test_AMI_finding() (toil.test.provisioners.aws.awsProvisionerTest.AWSProvisionerBenchTest method) test_atomic_context_error() (toil.test.src.miscTests.MiscTests method) test_atomic_context_ok() (toil.test.src.miscTests.MiscTests method) test_atomic_install() (toil.test.src.miscTests.MiscTests method) test_atomic_install_dev() (toil.test.src.miscTests.MiscTests method) test_available_cores() (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemTest method) test_basic_import_export() (toil.test.src.importExportFileTest.ImportExportFileTest method) test_batchsystem_plugin_installable() (toil.test.batchSystems.batch_system_plugin_test.BatchSystemPluginTest method) test_bioconda() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_biocontainers() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_build_tag() (toil.test.lib.aws.test_utils.TagGenerationTest method) test_build_tag_with_tags() (toil.test.lib.aws.test_utils.TagGenerationTest method) test_caching_option_priority() (toil.test.options.options.OptionsTest method) test_cactus_integration() (toil.test.cactus.test_cactus_integration.CactusIntegrationTest method) test_call_command_err() (toil.test.src.miscTests.MiscTests method) test_call_command_ok() (toil.test.src.miscTests.MiscTests method) test_chaining() (toil.test.src.resumabilityTest.ResumabilityTest method) test_coalesce() (toil.test.wdl.wdltoil_test.WDLTests method) test_coalesce_job_exit_codes_many_all_exist() (toil.test.batchSystems.test_slurm.SlurmTest method) test_coalesce_job_exit_codes_one_exists() (toil.test.batchSystems.test_slurm.SlurmTest method) test_coalesce_job_exit_codes_one_not_exists() (toil.test.batchSystems.test_slurm.SlurmTest method) test_coalesce_job_exit_codes_sacct_raises_job_exists() (toil.test.batchSystems.test_slurm.SlurmTest method) test_coalesce_job_exit_codes_sacct_raises_job_not_exists() (toil.test.batchSystems.test_slurm.SlurmTest method) test_coalesce_job_exit_codes_some_exists() (toil.test.batchSystems.test_slurm.SlurmTest method) test_config_functionality() (toil.test.utils.utilsTest.UtilsTest method) test_conformance_tests_integration() (toil.test.wdl.wdltoil_test.WDLConformanceTests method) test_conformance_tests_v10() (toil.test.wdl.wdltoil_test.WDLConformanceTests method) test_conformance_tests_v11() (toil.test.wdl.wdltoil_test.WDLConformanceTests method) test_convert() (toil.test.lib.test_conversions.ConversionTest method) test_create_bucket() (toil.test.lib.aws.test_s3.S3Test method) test_cross_thread_messaging() (toil.test.src.busTest.MessageBusTest method) test_cuda() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_cwl_cmdline_input() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_cwl_on_arm() (toil.test.provisioners.clusterTest.CWLOnARMTest method) test_cwl_toil_kill() (toil.test.utils.toilKillTest.ToilKillTest method) test_default_args() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_default_caching_slurm() (toil.test.options.options.OptionsTest method) test_download_directory_file() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_download_directory_s3() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_download_directory_s3_reference() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_download_file() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_download_http() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_download_https() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_download_https_reference() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_download_s3() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_download_structure() (in module toil.test.cwl.cwlTest) test_download_subdirectory_file() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_download_subdirectory_s3() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_empty_aws_tags() (toil.test.lib.aws.test_utils.TagGenerationTest method) test_enum_ints_in_file() (toil.test.src.busTest.MessageBusTest method) test_environment() (toil.test.src.environmentTest.EnvironmentTest method) test_fetch_arm_flatcar() (toil.test.lib.test_ec2.AMITest method) test_fetch_flatcar() (toil.test.lib.test_ec2.AMITest method) test_file_link_imports() (toil.test.jobStores.jobStoreTest.FileJobStoreTest method) test_filename_conflict_detection() (in module toil.test.cwl.cwlTest) test_filename_conflict_detection_at_root() (in module toil.test.cwl.cwlTest) test_filename_conflict_resolution() (in module toil.test.cwl.cwlTest) test_get_bucket_location_public_bucket() (toil.test.lib.aws.test_s3.S3Test method) test_get_policy_permissions() (toil.test.lib.aws.test_iam.IAMTest method) test_get_service_info() (toil.test.server.serverTest.ToilWESServerBenchTest method) test_get_user_name() (toil.test.lib.test_misc.UserNameAvailableTest method) (toil.test.lib.test_misc.UserNameUnvailableTest method) (toil.test.lib.test_misc.UserNameVeryBrokenTest method) test_getJobDetailsFromSacct_many_all_exist() (toil.test.batchSystems.test_slurm.SlurmTest method) test_getJobDetailsFromSacct_many_none_exist() (toil.test.batchSystems.test_slurm.SlurmTest method) test_getJobDetailsFromSacct_many_some_exist() (toil.test.batchSystems.test_slurm.SlurmTest method) test_getJobDetailsFromSacct_one_exists() (toil.test.batchSystems.test_slurm.SlurmTest method) test_getJobDetailsFromSacct_one_not_exists() (toil.test.batchSystems.test_slurm.SlurmTest method) test_getJobDetailsFromScontrol_many_all_exist() (toil.test.batchSystems.test_slurm.SlurmTest method) test_getJobDetailsFromScontrol_many_none_exist() (toil.test.batchSystems.test_slurm.SlurmTest method) test_getJobDetailsFromScontrol_many_some_exist() (toil.test.batchSystems.test_slurm.SlurmTest method) test_getJobDetailsFromScontrol_one_exists() (toil.test.batchSystems.test_slurm.SlurmTest method) test_getJobDetailsFromScontrol_one_not_exists() (toil.test.batchSystems.test_slurm.SlurmTest method) test_getJobExitCode_job_exists() (toil.test.batchSystems.test_slurm.SlurmTest method) test_getJobExitCode_job_not_exists() (toil.test.batchSystems.test_slurm.SlurmTest method) test_getJobExitCode_sacct_raises_job_exists() (toil.test.batchSystems.test_slurm.SlurmTest method) test_getJobExitCode_sacct_raises_job_not_exists() (toil.test.batchSystems.test_slurm.SlurmTest method) test_giraffe() (toil.test.wdl.wdltoil_test.WDLTests method) test_giraffe_deepvariant() (toil.test.wdl.wdltoil_test.WDLTests method) test_glob_dir_bypass_file_store() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_gridengine_cwl_conformance() (toil.test.cwl.cwlTest.CWLv10Test method) test_gridengine_cwl_conformance_with_caching() (toil.test.cwl.cwlTest.CWLv10Test method) test_gs_uri() (toil.test.wdl.wdltoil_test.WDLTests method) test_health() (toil.test.server.serverTest.ToilWESServerBenchTest method) test_hms_duration_to_seconds() (toil.test.lib.test_conversions.ConversionTest method) test_home() (toil.test.server.serverTest.ToilWESServerBenchTest method) test_human2bytes() (toil.test.lib.test_conversions.ConversionTest method) test_import_export_restart_false() (toil.test.src.importExportFileTest.ImportExportFileTest method) test_import_export_restart_true() (toil.test.src.importExportFileTest.ImportExportFileTest method) test_incorrect_json_emoji() (toil.test.lib.aws.test_utils.TagGenerationTest method) test_incorrect_json_object() (toil.test.lib.aws.test_utils.TagGenerationTest method) test_jobstore_does_not_leak_symlinks() (toil.test.jobStores.jobStoreTest.FileJobStoreTest method) test_jobstore_init_preserves_symlink_path() (toil.test.jobStores.jobStoreTest.FileJobStoreTest method) test_kubernetes_cwl_conformance() (toil.test.cwl.cwlTest.CWLv10Test method) (toil.test.cwl.cwlTest.CWLv11Test method) (toil.test.cwl.cwlTest.CWLv12Test method) test_kubernetes_cwl_conformance_with_caching() (toil.test.cwl.cwlTest.CWLv10Test method) (toil.test.cwl.cwlTest.CWLv11Test method) (toil.test.cwl.cwlTest.CWLv12Test method) test_label_constraints() (toil.test.batchSystems.batchSystemTest.KubernetesBatchSystemBenchTest method) test_load_contents_file() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_load_contents_http() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_load_contents_https() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_load_contents_s3() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_log_dir_echo_no_output() (in module toil.test.cwl.cwlTest) test_log_dir_echo_stderr() (in module toil.test.cwl.cwlTest) test_lsf_cwl_conformance() (toil.test.cwl.cwlTest.CWLv10Test method) test_lsf_cwl_conformance_with_caching() (toil.test.cwl.cwlTest.CWLv10Test method) test_MD5sum() (toil.test.wdl.wdltoil_test.WDLTests method) test_mesos_cwl_conformance() (toil.test.cwl.cwlTest.CWLv10Test method) test_mesos_cwl_conformance_with_caching() (toil.test.cwl.cwlTest.CWLv10Test method) test_miniwdl_self_test() (toil.test.wdl.wdltoil_test.WDLTests method) test_miniwdl_self_test_by_reference() (toil.test.wdl.wdltoil_test.WDLTests method) test_missing_output_directory() (toil.test.wdl.wdltoil_test.WDLTests method) test_mpi() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_negative_permissions_iam() (toil.test.lib.aws.test_iam.IAMTest method) test_nested_panic() (toil.test.src.miscTests.TestPanic method) test_node_type_parsing() (toil.test.provisioners.provisionerTest.ProvisionerTest method) test_omp_threads() (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemJobTest method) test_overhead_accounting_large() (toil.test.provisioners.clusterScalerTest.ClusterScalerTest method) test_overhead_accounting_observed() (toil.test.provisioners.clusterScalerTest.ClusterScalerTest method) test_overhead_accounting_small() (toil.test.provisioners.clusterScalerTest.ClusterScalerTest method) test_panic() (toil.test.src.miscTests.TestPanic method) test_panic_by_hand() (toil.test.src.miscTests.TestPanic method) test_panic_with_secondary() (toil.test.src.miscTests.TestPanic method) test_parse_archive_feed() (toil.test.lib.test_ec2.FlatcarFeedTest method) test_parse_beta_feed() (toil.test.lib.test_ec2.FlatcarFeedTest method) test_parse_mem_and_cmd_from_output() (toil.test.batchSystems.test_lsf_helper.LSFHelperTest method) test_parse_stable_feed() (toil.test.lib.test_ec2.FlatcarFeedTest method) test_permissions_iam() (toil.test.lib.aws.test_iam.IAMTest method) test_pick_value_with_one_null_value() (in module toil.test.cwl.cwlTest) test_preemptability_constraints() (toil.test.batchSystems.batchSystemTest.KubernetesBatchSystemBenchTest method) test_preemptible() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_preemptible_expression() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_print_job_info() (toil.test.utils.toilDebugTest.DebugJobTest method) test_read_write_global_files() (toil.test.provisioners.aws.awsProvisionerTest.AWSProvisionerBenchTest method) test_restart() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_restart_without_bus_path() (toil.test.src.busTest.MessageBusTest method) test_retrieve_task_directory() (toil.test.utils.toilDebugTest.DebugJobTest method) test_run_and_cancel_workflows() (toil.test.server.serverTest.ToilWESServerWorkflowTest method) test_run_colon_output() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_run_conformance() (toil.test.cwl.cwlTest.CWLv10Test method) (toil.test.cwl.cwlTest.CWLv11Test method) (toil.test.cwl.cwlTest.CWLv12Test method) test_run_conformance_with_caching() (toil.test.cwl.cwlTest.CWLv10Test method) (toil.test.cwl.cwlTest.CWLv11Test method) (toil.test.cwl.cwlTest.CWLv12Test method) test_run_conformance_with_in_place_update() (toil.test.cwl.cwlTest.CWLv12Test method) test_run_job() (toil.test.utils.toilDebugTest.DebugJobTest method) test_run_jobs() (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemTest method) test_run_revsort() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_run_revsort2() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_run_revsort_debug_worker() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_run_revsort_nochecksum() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_run_workflow_https_url() (toil.test.server.serverTest.ToilWESServerWorkflowTest method) test_run_workflow_inputs_zip() (toil.test.server.serverTest.ToilWESServerWorkflowTest method) test_run_workflow_manifest_and_inputs_zip() (toil.test.server.serverTest.ToilWESServerWorkflowTest method) test_run_workflow_manifest_zip() (toil.test.server.serverTest.ToilWESServerWorkflowTest method) test_run_workflow_multi_file_zip() (toil.test.server.serverTest.ToilWESServerWorkflowTest method) test_run_workflow_no_params_zip() (toil.test.server.serverTest.ToilWESServerWorkflowTest method) test_run_workflow_relative_url() (toil.test.server.serverTest.ToilWESServerWorkflowTest method) test_run_workflow_relative_url_no_attachments_fails() (toil.test.server.serverTest.ToilWESServerWorkflowTest method) test_run_workflow_single_file_zip() (toil.test.server.serverTest.ToilWESServerWorkflowTest method) test_s3_as_secondary_file() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_set_env() (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemTest method) test_set_job_env() (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemTest method) test_slurm_cwl_conformance() (toil.test.cwl.cwlTest.CWLv10Test method) test_slurm_cwl_conformance_with_caching() (toil.test.cwl.cwlTest.CWLv10Test method) test_state_store() (toil.test.server.serverTest.hidden.AbstractStateStoreTest method) test_state_store_paths() (toil.test.server.serverTest.AWSStateStoreTest method) test_streamable() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_streamable_reference() (toil.test.cwl.cwlTest.CWLWorkflowTest method) test_torque_cwl_conformance() (toil.test.cwl.cwlTest.CWLv10Test method) test_torque_cwl_conformance_with_caching() (toil.test.cwl.cwlTest.CWLv10Test method) test_visit_cwl_class_and_reduce() (in module toil.test.cwl.cwlTest) test_visit_top_cwl_class() (in module toil.test.cwl.cwlTest) test_wdl_kubernetes_cluster() (toil.test.wdl.wdltoil_test_kubernetes.WDLKubernetesClusterTest method) test_wes_server_cwl_conformance() (toil.test.cwl.cwlTest.CWLv12Test method) test_wildcard_handling() (toil.test.lib.aws.test_iam.IAMTest method) test_workflow_canceling_recovery() (toil.test.server.serverTest.ToilServerUtilsTest method) test_workflow_echo_string() (in module toil.test.cwl.cwlTest) test_workflow_echo_string_scatter_capture_stdout() (in module toil.test.cwl.cwlTest) test_workflow_echo_string_scatter_stderr_log_dir() (in module toil.test.cwl.cwlTest) test_yaml (toil.test.cwl.cwlTest.CWLv11Test attribute) (toil.test.cwl.cwlTest.CWLv12Test attribute) testAddChildEncapsulate() (toil.test.src.jobEncapsulationTest.JobEncapsulationTest method) testAddingInitialNode() (toil.test.provisioners.clusterScalerTest.BinPackingTest method) testAlways() (toil.test.src.retainTempDirTest.CleanWorkDirTest method) testApplianceParser() (toil.test.src.dockerCheckTest.DockerCheckTest method) testArguments() (toil.test.docs.scriptsTest.ToilDocumentationTest method) testAsyncWriteWithCaching() (toil.test.src.fileStoreTest.hidden.AbstractCachingFileStoreTest method) testAtomicityOfNonEmptyDirectoryRenames() (toil.test.src.systemTest.SystemTest method) testAutoScale() (toil.test.provisioners.aws.awsProvisionerTest.AWSAutoscaleTest method) (toil.test.provisioners.aws.awsProvisionerTest.AWSAutoscaleTestMultipleNodeTypes method) (toil.test.provisioners.gceProvisionerTest.GCEAutoscaleTest method) (toil.test.provisioners.gceProvisionerTest.GCEAutoscaleTestMultipleNodeTypes method) testAutoScaledCluster() (toil.test.provisioners.aws.awsProvisionerTest.AWSRestartTest method) (toil.test.provisioners.gceProvisionerTest.GCERestartTest method) testAwsMesos() (toil.test.sort.sortTest.SortTest method) testAWSProvisionerUtils() (toil.test.utils.utilsTest.UtilsTest method) testAwsSingle() (toil.test.sort.sortTest.SortTest method) testBadGoogleRepo() (toil.test.src.dockerCheckTest.DockerCheckTest method) testBadQuayRepo() (toil.test.src.dockerCheckTest.DockerCheckTest method) testBadQuayRepoNTag() (toil.test.src.dockerCheckTest.DockerCheckTest method) testBadQuayTag() (toil.test.src.dockerCheckTest.DockerCheckTest method) testBatchCreate() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testBatchSystemCleanupCanHandleWorkerDeaths() (toil.test.src.deferredFunctionTest.DeferredFunctionTest method) testBetaInertia() (toil.test.provisioners.clusterScalerTest.ClusterScalerTest method) testBroadDockerRepo() (toil.test.src.dockerCheckTest.DockerCheckTest method) testBroadDockerRepoBadTag() (toil.test.src.dockerCheckTest.DockerCheckTest method) testBuiltIn() (toil.test.src.resourceTest.ResourceTest method) testCacheEvictionFailCase() (toil.test.src.fileStoreTest.hidden.AbstractCachingFileStoreTest method) testCacheEvictionPartialEvict() (toil.test.src.fileStoreTest.hidden.AbstractCachingFileStoreTest method) testCacheEvictionTotalEvict() (toil.test.src.fileStoreTest.hidden.AbstractCachingFileStoreTest method) testCachingFileStore() (toil.test.src.jobFileStoreTest.JobFileStoreTest method) testCheckpointedRestartSucceeds() (toil.test.src.checkpointTest.CheckpointTest method) testCheckpointNotRetried() (toil.test.src.checkpointTest.CheckpointTest method) testCheckpointRetriedOnce() (toil.test.src.checkpointTest.CheckpointTest method) testCheckResourceRequest() (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemTest method) testChildLoadingEquality() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testCleanCache() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testClusterScaling() (toil.test.provisioners.clusterScalerTest.ScalerThreadTest method) testClusterScalingMultipleNodeTypes() (toil.test.provisioners.clusterScalerTest.ScalerThreadTest method) testClusterScalingWithPreemptibleJobs() (toil.test.provisioners.clusterScalerTest.ScalerThreadTest method) testConcurrencyDynamic() (toil.test.src.promisedRequirementTest.hidden.AbstractPromisedRequirementsTest method) testConcurrencyStatic() (toil.test.src.promisedRequirementTest.hidden.AbstractPromisedRequirementsTest method) testConcurrencyWithDisk() (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystemJobTest method) testConfigEquality() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testContextManger() (toil.test.src.toilContextManagerTest.ToilContextManagerTest method) testControlledFailedWorkerRetry() (toil.test.src.fileStoreTest.hidden.AbstractCachingFileStoreTest method) testCopySubRangeOfFile() (toil.test.sort.sortTest.SortTest method) testDAGConsistency() (toil.test.src.jobTest.JobTest method) testDeadlockDetection() (toil.test.src.jobTest.JobTest method) testDeferralWithConcurrentEncapsulation() (toil.test.src.autoDeploymentTest.AutoDeploymentTest method) testDeferralWithFailureAndEncapsulation() (toil.test.src.autoDeploymentTest.AutoDeploymentTest method) testDeferredFunctionRunsWithClassMethod() (toil.test.src.deferredFunctionTest.DeferredFunctionTest method) testDeferredFunctionRunsWithFailures() (toil.test.src.deferredFunctionTest.DeferredFunctionTest method) testDeferredFunctionRunsWithLambda() (toil.test.src.deferredFunctionTest.DeferredFunctionTest method) testDeferredFunctionRunsWithMethod() (toil.test.src.deferredFunctionTest.DeferredFunctionTest method) testDeleteLocalFile() (toil.test.src.fileStoreTest.hidden.AbstractCachingFileStoreTest method) testDestructionIdempotence() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testDestructionOfCorruptedJobStore() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testDocker() (toil.test.docs.scriptsTest.ToilDocumentationTest method) testDockerClean() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_CRx_FORGO() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_CRx_None() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_CRx_RM() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_CRx_STOP() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_CxD_FORGO() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_CxD_None() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_CxD_RM() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_CxD_STOP() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_Cxx_FORGO() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_Cxx_None() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_Cxx_RM() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_Cxx_STOP() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_xRx_FORGO() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_xRx_None() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_xRx_RM() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_xRx_STOP() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_xxD_FORGO() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_xxD_None() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_xxD_RM() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_xxD_STOP() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_xxx_FORGO() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_xxx_None() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_xxx_RM() (toil.test.lib.dockerTest.DockerTest method) testDockerClean_xxx_STOP() (toil.test.lib.dockerTest.DockerTest method) testDockerLogs() (toil.test.lib.dockerTest.DockerTest method) testDockerLogs_Demux() (toil.test.lib.dockerTest.DockerTest method) testDockerLogs_Demux_Stream() (toil.test.lib.dockerTest.DockerTest method) testDockerLogs_Stream() (toil.test.lib.dockerTest.DockerTest method) testDockerPipeChain() (toil.test.lib.dockerTest.DockerTest method) testDockerPipeChainErrorDetection() (toil.test.lib.dockerTest.DockerTest method) testDynamic() (toil.test.docs.scriptsTest.ToilDocumentationTest method) testEmptyFileStoreIDIsReadable() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testEncapsulation() (toil.test.docs.scriptsTest.ToilDocumentationTest method) (toil.test.src.jobEncapsulationTest.JobEncapsulationTest method) testEncapsulation2() (toil.test.docs.scriptsTest.ToilDocumentationTest method) testEncrypted() (toil.test.jobStores.jobStoreTest.AbstractEncryptedJobStoreTest.Test method) TesterFuncType (in module toil.test.cwl.cwlTest) testEvaluatingRandomDAG() (toil.test.src.jobTest.JobTest method) testExportAfterFailedExport() (toil.test.src.toilContextManagerTest.ToilContextManagerTest method) testExtremeCacheSetup() (toil.test.src.fileStoreTest.hidden.AbstractCachingFileStoreTest method) testFetchJobStoreFiles() (in module toil.test.utils.toilDebugTest) testFileDeletion() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testFileGridEngine() (toil.test.sort.sortTest.SortTest method) testFileMesos() (toil.test.sort.sortTest.SortTest method) testFileSingle() (toil.test.sort.sortTest.SortTest method) testFileSingle10000() (toil.test.sort.sortTest.SortTest method) testFileSingleCheckpoints() (toil.test.sort.sortTest.SortTest method) testFileSingleNonCaching() (toil.test.sort.sortTest.SortTest method) testFileStoreExportFile() (toil.test.src.fileStoreTest.hidden.AbstractCachingFileStoreTest method) testFileStoreLogging() (toil.test.src.fileStoreTest.hidden.AbstractFileStoreTest method) testFileStoreOperations() (toil.test.src.fileStoreTest.hidden.AbstractFileStoreTest method) testFileTorqueEngine() (toil.test.sort.sortTest.SortTest method) testGetMidPoint() (toil.test.sort.sortTest.SortTest method) testGetPIDStatus() (toil.test.utils.utilsTest.UtilsTest method) testGetSizeOfDirectoryWorks() (toil.test.src.miscTests.MiscTests method) testGetStatusFailedCWLWF() (toil.test.utils.utilsTest.UtilsTest method) testGetStatusFailedToilWF() (toil.test.utils.utilsTest.UtilsTest method) testGetStatusSuccessfulCWLWF() (toil.test.utils.utilsTest.UtilsTest method) testGlobalMutexOrdering() (toil.test.src.threadingTest.ThreadingTest method) testGoogleMesos() (toil.test.sort.sortTest.SortTest method) testGoogleRepo() (toil.test.src.dockerCheckTest.DockerCheckTest method) testGoogleSingle() (toil.test.sort.sortTest.SortTest method) testGrowingAndShrinkingJob() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testHelloworld() (toil.test.docs.scriptsTest.ToilDocumentationTest method) testHelloWorld() (toil.test.src.helloWorldTest.HelloWorldTest method) testHidingProcessEscape() (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystemTest method) testHighTargetTime() (toil.test.provisioners.clusterScalerTest.BinPackingTest method) testIDStability() (toil.test.src.miscTests.MiscTests method) testIgnoreNode() (toil.test.batchSystems.batchSystemTest.MesosBatchSystemTest method) testImportFtpFile() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testImportHttpFile() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testImportReadFileCompatibility() (toil.test.src.fileStoreTest.hidden.AbstractFileStoreTest method) testingIsAutomatic (in module toil.test.src.fileStoreTest) testInitialState() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testInlinedFiles() (toil.test.jobStores.jobStoreTest.AWSJobStoreTest method) testInvalidJobStoreName() (toil.test.jobStores.jobStoreTest.InvalidAWSJobStoreTest method) testInvokeworkflow() (toil.test.docs.scriptsTest.ToilDocumentationTest method) testInvokeworkflow2() (toil.test.docs.scriptsTest.ToilDocumentationTest method) testJobClass() (toil.test.src.userDefinedJobArgTypeTest.UserDefinedJobArgTypeTest method) testJobClassFromMain() (toil.test.src.userDefinedJobArgTypeTest.UserDefinedJobArgTypeTest method) testJobConcurrency() (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemJobTest method) testJobCreation() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testJobDeletions() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testJobDescription() (toil.test.src.jobDescriptionTest.JobDescriptionTest method) testJobDescriptionSequencing() (toil.test.src.jobDescriptionTest.JobDescriptionTest method) testJobFileStore() (toil.test.src.jobFileStoreTest.JobFileStoreTest method) testJobFileStoreWithBadWorker() (toil.test.src.jobFileStoreTest.JobFileStoreTest method) testJobFunction() (toil.test.src.userDefinedJobArgTypeTest.UserDefinedJobArgTypeTest method) testJobFunctionFromMain() (toil.test.src.userDefinedJobArgTypeTest.UserDefinedJobArgTypeTest method) testJobFunctions() (toil.test.docs.scriptsTest.ToilDocumentationTest method) testJobLoadEquality() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testJobQueue() (toil.test.mesos.MesosDataStructuresTest.DataStructuresTest method) testJobStoreContents() (in module toil.test.utils.toilDebugTest) testJobTooLargeForAllNodes() (toil.test.provisioners.clusterScalerTest.BinPackingTest method) testLargeFile() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testLastProcessStanding() (toil.test.src.threadingTest.ThreadingTest method) testLogToMaster() (toil.test.src.regularLogTest.RegularLogTest method) testLongRunningJobs() (toil.test.provisioners.clusterScalerTest.BinPackingTest method) testLowTargetTime() (toil.test.provisioners.clusterScalerTest.BinPackingTest method) testManaging() (toil.test.docs.scriptsTest.ToilDocumentationTest method) testManaging2() (toil.test.docs.scriptsTest.ToilDocumentationTest method) testMaxNodes() (toil.test.provisioners.clusterScalerTest.ClusterScalerTest method) testMerge() (toil.test.sort.sortTest.SortTest method) testMinNodes() (toil.test.provisioners.clusterScalerTest.ClusterScalerTest method) testMultipartUploads() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testMultiplejobs() (toil.test.docs.scriptsTest.ToilDocumentationTest method) testMultiplejobs2() (toil.test.docs.scriptsTest.ToilDocumentationTest method) testMultiplejobs3() (toil.test.docs.scriptsTest.ToilDocumentationTest method) testMultipleJobsPerWorkerStats() (toil.test.utils.utilsTest.UtilsTest method) testMultipleJobsReadSameCacheHitGlobalFile() (toil.test.src.fileStoreTest.hidden.AbstractCachingFileStoreTest method) testMultipleJobsReadSameCacheMissGlobalFile() (toil.test.src.fileStoreTest.hidden.AbstractCachingFileStoreTest method) testMultipleLogToMaster() (toil.test.src.regularLogTest.RegularLogTest method) testMultiThreadImportFile() (toil.test.jobStores.jobStoreTest.AWSJobStoreTest method) testNestedResourcesDoNotBlock() (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystemJobTest method) testNever() (toil.test.src.retainTempDirTest.CleanWorkDirTest method) testNewCheckpointIsLeafVertexNonRootCase() (toil.test.src.jobTest.JobTest method) testNewCheckpointIsLeafVertexRootCase() (toil.test.src.jobTest.JobTest method) testNewJobsCanHandleOtherJobDeaths() (toil.test.src.deferredFunctionTest.DeferredFunctionTest method) testNextChainable() (toil.test.src.workerTest.WorkerTests method) testNo (toil.test.sort.sortTest.SortTest attribute) testNoContextManger() (toil.test.src.toilContextManagerTest.ToilContextManagerTest method) testNoLaunchingIfDeltaAlreadyMet() (toil.test.provisioners.clusterScalerTest.ClusterScalerTest method) testNonCachingDockerChain() (toil.test.lib.dockerTest.DockerTest method) testNonCachingDockerChainErrorDetection() (toil.test.lib.dockerTest.DockerTest method) testNonCachingFileStore() (toil.test.src.jobFileStoreTest.JobFileStoreTest method) testNonexistentRepo() (toil.test.src.dockerCheckTest.DockerCheckTest method) testNonPyStandAlone() (toil.test.src.resourceTest.ResourceTest method) testOfficialUbuntuRepo() (toil.test.src.dockerCheckTest.DockerCheckTest method) testOnErrorWithError() (toil.test.src.retainTempDirTest.CleanWorkDirTest method) testOnErrorWithNoError() (toil.test.src.retainTempDirTest.CleanWorkDirTest method) testOnSuccessWithError() (toil.test.src.retainTempDirTest.CleanWorkDirTest method) testOnSuccessWithSuccess() (toil.test.src.retainTempDirTest.CleanWorkDirTest method) testOverlargeJob() (toil.test.jobStores.jobStoreTest.AWSJobStoreTest method) testPackage() (toil.test.src.resourceTest.ResourceTest method) testPackingOneShape() (toil.test.provisioners.clusterScalerTest.BinPackingTest method) TestPanic (class in toil.test.src.miscTests) testPartialReadFromStream() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method)

testPathologicalCase() (toil.test.provisioners.clusterScalerTest.BinPackingTest method) testPerJobFiles() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testPersistantFilesToDelete() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testPreemptibleDeficitIsSet() (toil.test.provisioners.clusterScalerTest.ClusterScalerTest method) testPreemptibleDeficitResponse() (toil.test.provisioners.clusterScalerTest.ClusterScalerTest method) testPreserveFileName() (toil.test.jobStores.jobStoreTest.FileJobStoreTest method) testPrintJobLog() (toil.test.utils.utilsTest.UtilsTest method) testProcessEscape() (toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystemTest method) testPromiseRequirementRaceStatic() (toil.test.src.promisedRequirementTest.hidden.AbstractPromisedRequirementsTest method) testPromises() (toil.test.docs.scriptsTest.ToilDocumentationTest method) testPromises2() (toil.test.docs.scriptsTest.ToilDocumentationTest method) testPromisesWithJobStoreFileObjects() (toil.test.src.promisedRequirementTest.hidden.AbstractPromisedRequirementsTest method) testPromisesWithNonCachingFileStore() (toil.test.src.promisedRequirementTest.hidden.AbstractPromisedRequirementsTest method) testQuickstart() (toil.test.docs.scriptsTest.ToilDocumentationTest method) testReadCacheMissFileFromJobStoreWithCachingReadFile() (toil.test.src.fileStoreTest.hidden.AbstractCachingFileStoreTest method) testReadCacheMissFileFromJobStoreWithoutCachingReadFile() (toil.test.src.fileStoreTest.hidden.AbstractCachingFileStoreTest method) testReadCachHitFileFromJobStore() (toil.test.src.fileStoreTest.hidden.AbstractCachingFileStoreTest method) testReadWriteFileStreamTextMode() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) (toil.test.src.fileStoreTest.hidden.AbstractFileStoreTest method) testReadWriteSharedFilesTextMode() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testRealtimeLogger() (toil.test.src.realtimeLoggerTest.RealtimeLoggerTest method) testRegularLog() (toil.test.src.regularLogTest.RegularLogTest method) testRemoveLocalImmutablyReadFile() (toil.test.src.fileStoreTest.hidden.AbstractCachingFileStoreTest method) testRemoveLocalMutablyReadFile() (toil.test.src.fileStoreTest.hidden.AbstractCachingFileStoreTest method) testRequirements() (toil.test.docs.scriptsTest.ToilDocumentationTest method) testRestart() (toil.test.src.autoDeploymentTest.AutoDeploymentTest method) testRestartAttribute() (toil.test.utils.utilsTest.UtilsTest method) testRestartedWorkflowSchedulesCorrectJobsOnFailedParent() (toil.test.src.restartDAGTest.RestartDAGTest method) testRestartedWorkflowSchedulesCorrectJobsOnKilledParent() (toil.test.src.restartDAGTest.RestartDAGTest method) testReturnFileSizes() (toil.test.src.fileStoreTest.hidden.AbstractCachingFileStoreTest method) testReturnFileSizesWithBadWorker() (toil.test.src.fileStoreTest.hidden.AbstractCachingFileStoreTest method) testRounding() (toil.test.provisioners.clusterScalerTest.ClusterScalerTest method) testScalableBatchSystem() (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemTest method) testSDBDomainsDeletedOnFailedJobstoreBucketCreation() (toil.test.jobStores.jobStoreTest.AWSJobStoreTest method) testService() (toil.test.src.jobServiceTest.JobServiceTest method) testServiceDeadlock() (toil.test.src.jobServiceTest.JobServiceTest method) testServiceParallelRecursive() (toil.test.src.jobServiceTest.JobServiceTest method) testServiceRecursive() (toil.test.src.jobServiceTest.JobServiceTest method) testServices() (toil.test.batchSystems.batchSystemTest.MaxCoresSingleMachineBatchSystemTest method) (toil.test.docs.scriptsTest.ToilDocumentationTest method) testServiceSerialization() (toil.test.src.jobServiceTest.JobServiceTest method) testServiceWithCheckpoints() (toil.test.src.jobServiceTest.JobServiceTest method) testSharedFiles() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testSiblingDAGConsistency() (toil.test.src.jobTest.JobTest method) testSimultaneousReadsUncachedStream() (toil.test.src.fileStoreTest.hidden.AbstractCachingFileStoreTest method) testSort() (toil.test.sort.sortTest.SortTest method) testSorting() (toil.test.provisioners.clusterScalerTest.BinPackingTest method) testSplitRootPackages() (toil.test.src.autoDeploymentTest.AutoDeploymentTest method) testSpotAutoScale() (toil.test.provisioners.aws.awsProvisionerTest.AWSAutoscaleTest method) (toil.test.provisioners.gceProvisionerTest.GCEAutoscaleTest method) testSpotAutoScaleBalancingTypes() (toil.test.provisioners.aws.awsProvisionerTest.AWSAutoscaleTest method) testStaging() (toil.test.docs.scriptsTest.ToilDocumentationTest method) testStandAlone() (toil.test.src.resourceTest.ResourceTest method) testStandAloneInPackage() (toil.test.src.resourceTest.ResourceTest method) testStatic() (toil.test.src.jobTest.JobTest method) testStatic2() (toil.test.src.jobTest.JobTest method) testStats() (toil.test.docs.scriptsTest.ToilDocumentationTest method) testStatsAndLogging() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testToilIsNotBroken() (toil.test.src.fileStoreTest.hidden.AbstractFileStoreTest method) testToilQuayRepo() (toil.test.src.dockerCheckTest.DockerCheckTest method) testTrivialDAGConsistency() (toil.test.src.jobTest.JobTest method) testUnicodeSupport() (toil.test.utils.utilsTest.UtilsTest method) testUpdateBehavior() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testUserTypesInJobFunctionArgs() (toil.test.src.autoDeploymentTest.AutoDeploymentTest method) testUtilsSort() (toil.test.utils.utilsTest.UtilsTest method) testUtilsStatsSort() (toil.test.utils.utilsTest.UtilsTest method) testVirtualEnv() (toil.test.src.resourceTest.ResourceTest method) testWriteExportFileCompatibility() (toil.test.src.fileStoreTest.hidden.AbstractFileStoreTest method) testWriteGzipLogs() (toil.test.src.regularLogTest.RegularLogTest method) testWriteLocalFileToJobStore() (toil.test.src.fileStoreTest.hidden.AbstractCachingFileStoreTest method) testWriteLogFiles() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testWriteLogs() (toil.test.src.regularLogTest.RegularLogTest method) testWriteNonLocalFileToJobStore() (toil.test.src.fileStoreTest.hidden.AbstractCachingFileStoreTest method) testWriteReadGlobalFilePermissions() (toil.test.src.fileStoreTest.hidden.AbstractFileStoreTest method) testZeroLengthFiles() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method) testZeroResourceJobs() (toil.test.provisioners.clusterScalerTest.BinPackingTest method) then_namespace() (toil.wdl.wdltoil.WDLBaseJob method) then_overlay() (toil.wdl.wdltoil.WDLBaseJob method) then_remove() (toil.wdl.wdltoil.WDLBaseJob method) then_underlay() (toil.wdl.wdltoil.WDLBaseJob method) ThreadingTest (class in toil.test.src.threadingTest) throttle (class in toil.lib.throttle) (class in toil.provisioners.clusterScaler) (class in toil.serviceManager) throttle() (toil.leader.LocalThrottle method) (toil.lib.throttle.LocalThrottle method) (toil.serviceManager.LocalThrottle method) THROTTLED_ERROR_CODES (in module toil.lib.aws.utils) TIME_CATEGORIES (in module toil.utils.toilStats) timeLimit() (in module toil.test) (in module toil.test.provisioners.aws.awsProvisionerTest) (in module toil.test.provisioners.gceProvisionerTest) title() (toil.utils.toilStats.ColumnWidths method) TITLES (in module toil.utils.toilStats) to_string() (toil.batchSystems.abstractBatchSystem.BatchJobExitReason class method) (toil.batchSystems.abstractGridEngineBatchSystem.BatchJobExitReason class method) (toil.batchSystems.awsBatch.BatchJobExitReason class method) (toil.batchSystems.kubernetes.BatchJobExitReason class method) (toil.batchSystems.lsf.BatchJobExitReason class method) (toil.batchSystems.mesos.batchSystem.BatchJobExitReason class method) (toil.batchSystems.slurm.BatchJobExitReason class method) (toil.leader.BatchJobExitReason class method) (toil.test.batchSystems.test_slurm.BatchJobExitReason class method) (toil.test.src.busTest.BatchJobExitReason class method) toCommand() (toil.deferred.ModuleDescriptor method) (toil.job.ModuleDescriptor method) (toil.resource.ModuleDescriptor method) (toil.test.src.jobDescriptionTest.ModuleDescriptor method) (toil.test.src.resourceTest.ModuleDescriptor method) toIgnitionConfig() (toil.leader.AbstractProvisioner.InstanceConfiguration method) (toil.provisioners.abstractProvisioner.AbstractProvisioner.InstanceConfiguration method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner.InstanceConfiguration method) (toil.provisioners.clusterScaler.AbstractProvisioner.InstanceConfiguration method) (toil.provisioners.gceProvisioner.AbstractProvisioner.InstanceConfiguration method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner.InstanceConfiguration method) toil module Toil (class in toil.batchSystems.abstractBatchSystem) (class in toil.batchSystems.awsBatch) (class in toil.batchSystems.cleanup_support) (class in toil.batchSystems.kubernetes) (class in toil.batchSystems.singleMachine) (class in toil.common) (class in toil.cwl.cwltoil) (class in toil.fileStores.abstractFileStore) (class in toil.job) (class in toil.server.wes.tasks) (class in toil.test.batchSystems.batch_system_plugin_test) (class in toil.test.batchSystems.batchSystemTest) (class in toil.test.jobStores.jobStoreTest) (class in toil.test.lib.dockerTest) (class in toil.test.mesos.helloWorld) (class in toil.test.options.options) (class in toil.test.sort.restart_sort) (class in toil.test.sort.sort) (class in toil.test.sort.sortTest) (class in toil.test.src.busTest) (class in toil.test.src.environmentTest) (class in toil.test.src.fileStoreTest) (class in toil.test.src.importExportFileTest) (class in toil.test.src.jobDescriptionTest) (class in toil.test.src.jobFileStoreTest) (class in toil.test.src.jobTest) (class in toil.test.src.restartDAGTest) (class in toil.test.src.toilContextManagerTest) (class in toil.test.utils.toilKillTest) (class in toil.test.utils.utilsTest) (class in toil.utils.toilClean) (class in toil.utils.toilDebugFile) (class in toil.utils.toilDebugJob) (class in toil.utils.toilKill) (class in toil.utils.toilStats) (class in toil.utils.toilStatus) (class in toil.wdl.wdltoil) (class in toil.worker) toil.batchSystems module toil.batchSystems.abstractBatchSystem module toil.batchSystems.abstractGridEngineBatchSystem module toil.batchSystems.awsBatch module toil.batchSystems.cleanup_support module toil.batchSystems.contained_executor module toil.batchSystems.gridengine module toil.batchSystems.htcondor module toil.batchSystems.kubernetes module toil.batchSystems.local_support module toil.batchSystems.lsf module toil.batchSystems.lsfHelper module toil.batchSystems.mesos module toil.batchSystems.mesos.batchSystem module toil.batchSystems.mesos.conftest module toil.batchSystems.mesos.executor module toil.batchSystems.mesos.test module toil.batchSystems.options module toil.batchSystems.registry module toil.batchSystems.singleMachine module toil.batchSystems.slurm module toil.batchSystems.torque module toil.bus module toil.common module toil.cwl module toil.cwl.conftest module toil.cwl.cwltoil module toil.cwl.utils module toil.deferred module toil.exceptions module toil.fileStores module toil.fileStores.abstractFileStore module toil.fileStores.cachingFileStore module toil.fileStores.nonCachingFileStore module toil.job module toil.jobStores module toil.jobStores.abstractJobStore module toil.jobStores.aws module toil.jobStores.aws.jobStore module toil.jobStores.aws.utils module toil.jobStores.conftest module toil.jobStores.fileJobStore module toil.jobStores.googleJobStore module toil.jobStores.utils module toil.leader module toil.lib module toil.lib.accelerators module toil.lib.aws module toil.lib.aws.ami module toil.lib.aws.iam module toil.lib.aws.session module toil.lib.aws.utils module toil.lib.bioio module toil.lib.compatibility module toil.lib.conversions module toil.lib.docker module toil.lib.ec2 module toil.lib.ec2nodes module toil.lib.encryption module toil.lib.encryption.conftest module toil.lib.exceptions module toil.lib.expando module toil.lib.generatedEC2Lists module toil.lib.humanize module toil.lib.io module toil.lib.iterables module toil.lib.memoize module toil.lib.misc module toil.lib.objects module toil.lib.resources module toil.lib.retry module toil.lib.threading module toil.lib.throttle module toil.options module toil.options.common module toil.options.cwl module toil.options.wdl module toil.provisioners module toil.provisioners.abstractProvisioner module toil.provisioners.aws module toil.provisioners.aws.awsProvisioner module toil.provisioners.clusterScaler module toil.provisioners.gceProvisioner module toil.provisioners.node module toil.realtimeLogger module toil.resource module toil.server module toil.server.api_spec module toil.server.app module toil.server.celery_app module toil.server.cli module toil.server.cli.wes_cwl_runner module toil.server.utils module toil.server.wes module toil.server.wes.abstract_backend module toil.server.wes.amazon_wes_utils module toil.server.wes.tasks module toil.server.wes.toil_backend module toil.server.wsgi_app module toil.serviceManager module toil.statsAndLogging module toil.test module toil.test.batchSystems module toil.test.batchSystems.batch_system_plugin_test module toil.test.batchSystems.batchSystemTest module toil.test.batchSystems.test_lsf_helper module toil.test.batchSystems.test_slurm module toil.test.cactus module toil.test.cactus.test_cactus_integration module toil.test.cwl module toil.test.cwl.conftest module toil.test.cwl.cwlTest module toil.test.docs module toil.test.docs.scriptsTest module toil.test.jobStores module toil.test.jobStores.jobStoreTest module toil.test.lib module toil.test.lib.aws module toil.test.lib.aws.test_iam module toil.test.lib.aws.test_s3 module toil.test.lib.aws.test_utils module toil.test.lib.dockerTest module toil.test.lib.test_conversions module toil.test.lib.test_ec2 module toil.test.lib.test_misc module toil.test.mesos module toil.test.mesos.helloWorld module toil.test.mesos.MesosDataStructuresTest module toil.test.mesos.stress module toil.test.options module toil.test.options.options module toil.test.provisioners module toil.test.provisioners.aws module toil.test.provisioners.aws.awsProvisionerTest module toil.test.provisioners.clusterScalerTest module toil.test.provisioners.clusterTest module toil.test.provisioners.gceProvisionerTest module toil.test.provisioners.provisionerTest module toil.test.provisioners.restartScript module toil.test.server module toil.test.server.serverTest module toil.test.sort module toil.test.sort.restart_sort module toil.test.sort.sort module toil.test.sort.sortTest module toil.test.src module toil.test.src.autoDeploymentTest module toil.test.src.busTest module toil.test.src.checkpointTest module toil.test.src.deferredFunctionTest module toil.test.src.dockerCheckTest module toil.test.src.environmentTest module toil.test.src.fileStoreTest module toil.test.src.helloWorldTest module toil.test.src.importExportFileTest module toil.test.src.jobDescriptionTest module toil.test.src.jobEncapsulationTest module toil.test.src.jobFileStoreTest module toil.test.src.jobServiceTest module toil.test.src.jobTest module toil.test.src.miscTests module toil.test.src.promisedRequirementTest module toil.test.src.promisesTest module toil.test.src.realtimeLoggerTest module toil.test.src.regularLogTest module toil.test.src.resourceTest module toil.test.src.restartDAGTest module toil.test.src.resumabilityTest module toil.test.src.retainTempDirTest module toil.test.src.systemTest module toil.test.src.threadingTest module toil.test.src.toilContextManagerTest module toil.test.src.userDefinedJobArgTypeTest module toil.test.src.workerTest module toil.test.utils module toil.test.utils.toilDebugTest module toil.test.utils.toilKillTest module toil.test.utils.utilsTest module toil.test.wdl module toil.test.wdl.wdltoil_test module toil.test.wdl.wdltoil_test_kubernetes module toil.toilState module toil.utils module toil.utils.toilClean module toil.utils.toilConfig module toil.utils.toilDebugFile module toil.utils.toilDebugJob module toil.utils.toilDestroyCluster module toil.utils.toilKill module toil.utils.toilLaunchCluster module toil.utils.toilMain module toil.utils.toilRsyncCluster module toil.utils.toilServer module toil.utils.toilSshCluster module toil.utils.toilStats module toil.utils.toilStatus module toil.utils.toilUpdateEC2Instances module toil.version module toil.wdl module toil.wdl.utils module toil.wdl.wdltoil module toil.worker module toil_batch_id (toil.batchSystems.abstractGridEngineBatchSystem.ExternalBatchIdMessage attribute) (toil.batchSystems.awsBatch.ExternalBatchIdMessage attribute) (toil.batchSystems.singleMachine.ExternalBatchIdMessage attribute) (toil.bus.ExternalBatchIdMessage attribute) (toil.bus.JobIssuedMessage attribute) (toil.bus.JobStatus attribute) (toil.common.JobIssuedMessage attribute) (toil.leader.JobIssuedMessage attribute) (toil.server.wes.amazon_wes_utils.JobStatus attribute) (toil.server.wes.toil_backend.JobStatus attribute) (toil.test.src.busTest.JobIssuedMessage attribute) toil_get_file() (in module toil.cwl.cwltoil) TOIL_HOME_DIR (in module toil.common) toil_logger (in module toil.statsAndLogging) toil_make_tool() (in module toil.cwl.cwltoil) toil_read_source() (in module toil.wdl.wdltoil) toil_service_env_options() (toil.leader.AbstractProvisioner method) (toil.provisioners.abstractProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AbstractProvisioner method) (toil.provisioners.aws.awsProvisioner.AWSProvisioner method) (toil.provisioners.clusterScaler.AbstractProvisioner method) (toil.provisioners.gceProvisioner.AbstractProvisioner method) (toil.test.provisioners.aws.awsProvisionerTest.AWSProvisioner method) (toil.test.provisioners.clusterScalerTest.AbstractProvisioner method) TOIL_URI_SCHEME (in module toil.wdl.wdltoil) ToilBackend (class in toil.server.app) (class in toil.server.wes.toil_backend) ToilCommandLineTool (class in toil.cwl.cwltoil) ToilContextManagerException, [1] ToilContextManagerTest (class in toil.test.src.toilContextManagerTest) ToilDocumentationTest (class in toil.test.docs.scriptsTest) ToilExpressionTool (class in toil.cwl.cwltoil) ToilFsAccess (class in toil.cwl.cwltoil) ToilJob (in module toil.batchSystems.mesos) (in module toil.batchSystems.mesos.batchSystem) ToilKillTest (class in toil.test.utils.toilKillTest) ToilKillTestWithAWSJobStore (class in toil.test.utils.toilKillTest) toilMain (toil.test.utils.utilsTest.UtilsTest property) ToilMetrics (class in toil.common) (class in toil.leader) toilPackageDirPath() (in module toil) (in module toil.test) ToilPathMapper (class in toil.cwl.cwltoil) ToilRestartException ToilServerUtilsTest (class in toil.test.server.serverTest) ToilSingleJobExecutor (class in toil.cwl.cwltoil) toilStageFiles() (in module toil.cwl.cwltoil) ToilState (class in toil.leader) (class in toil.serviceManager) (class in toil.toilState) ToilStatus (class in toil.test.utils.utilsTest) (class in toil.utils.toilDebugJob) (class in toil.utils.toilStatus) ToilTest (class in toil.test) (class in toil.test.batchSystems.batch_system_plugin_test) (class in toil.test.batchSystems.batchSystemTest) (class in toil.test.batchSystems.test_lsf_helper) (class in toil.test.batchSystems.test_slurm) (class in toil.test.cwl.cwlTest) (class in toil.test.docs.scriptsTest) (class in toil.test.jobStores.jobStoreTest) (class in toil.test.lib.aws.test_iam) (class in toil.test.lib.aws.test_s3) (class in toil.test.lib.aws.test_utils) (class in toil.test.lib.dockerTest) (class in toil.test.lib.test_conversions) (class in toil.test.lib.test_ec2) (class in toil.test.lib.test_misc) (class in toil.test.mesos.MesosDataStructuresTest) (class in toil.test.options.options) (class in toil.test.provisioners.aws.awsProvisionerTest) (class in toil.test.provisioners.clusterScalerTest) (class in toil.test.provisioners.clusterTest) (class in toil.test.provisioners.gceProvisionerTest) (class in toil.test.provisioners.provisionerTest) (class in toil.test.server.serverTest) (class in toil.test.sort.sortTest) (class in toil.test.src.busTest) (class in toil.test.src.checkpointTest) (class in toil.test.src.deferredFunctionTest) (class in toil.test.src.dockerCheckTest) (class in toil.test.src.environmentTest) (class in toil.test.src.fileStoreTest) (class in toil.test.src.helloWorldTest) (class in toil.test.src.importExportFileTest) (class in toil.test.src.jobDescriptionTest) (class in toil.test.src.jobEncapsulationTest) (class in toil.test.src.jobFileStoreTest) (class in toil.test.src.jobServiceTest) (class in toil.test.src.jobTest) (class in toil.test.src.miscTests) (class in toil.test.src.promisesTest) (class in toil.test.src.realtimeLoggerTest) (class in toil.test.src.regularLogTest) (class in toil.test.src.resourceTest) (class in toil.test.src.restartDAGTest) (class in toil.test.src.resumabilityTest) (class in toil.test.src.retainTempDirTest) (class in toil.test.src.systemTest) (class in toil.test.src.threadingTest) (class in toil.test.src.toilContextManagerTest) (class in toil.test.src.userDefinedJobArgTypeTest) (class in toil.test.src.workerTest) (class in toil.test.utils.toilDebugTest) (class in toil.test.utils.toilKillTest) (class in toil.test.utils.utilsTest) (class in toil.test.wdl.wdltoil_test) ToilTool (class in toil.cwl.cwltoil) ToilWDLStdLibBase (class in toil.wdl.wdltoil) ToilWDLStdLibTaskCommand (class in toil.wdl.wdltoil) ToilWDLStdLibTaskOutputs (class in toil.wdl.wdltoil) ToilWESServerBenchTest (class in toil.test.server.serverTest) ToilWESServerCeleryS3StateWorkflowTest (class in toil.test.server.serverTest) ToilWESServerCeleryWorkflowTest (class in toil.test.server.serverTest) ToilWESServerWorkflowTest (class in toil.test.server.serverTest) ToilWorkflow (class in toil.server.wes.toil_backend) ToilWorkflowRunner (class in toil.server.wes.tasks) toItem() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo method) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo method) tokenize_conf_stream() (in module toil.batchSystems.lsfHelper) tolerated_taints (toil.batchSystems.kubernetes.KubernetesBatchSystem.Placement attribute) topological_order() (toil.test.wdl.wdltoil_test.WDLWorkflowGraph method) (toil.wdl.wdltoil.WDLWorkflowGraph method) torque_batch_system_factory() (in module toil.batchSystems.registry) TorqueBatchSystem (class in toil.batchSystems.torque) TorqueBatchSystem.GridEngineThread (class in toil.batchSystems.torque) TorqueBatchSystemTest (class in toil.test.batchSystems.batchSystemTest) touchFile() (in module toil.test.mesos.stress) ToySerializableService (class in toil.test.src.jobServiceTest) ToyService (class in toil.test.src.jobServiceTest) transform() (toil.jobStores.aws.jobStore.ReadableTransformingPipe method) (toil.jobStores.utils.ReadableTransformingPipe method) traverseJobGraph() (toil.test.utils.utilsTest.ToilStatus method) (toil.utils.toilDebugJob.ToilStatus method) (toil.utils.toilStatus.ToilStatus method) trivialParent() (in module toil.test.src.jobTest) TrivialService (class in toil.test.src.jobTest) truncExpBackoff() (in module toil.jobStores.googleJobStore) (in module toil.lib.misc) (in module toil.provisioners.aws.awsProvisioner) try_and_nested_panic_with_secondary() (toil.test.src.miscTests.TestPanic method) try_and_panic() (toil.test.src.miscTests.TestPanic method) try_and_panic_by_hand() (toil.test.src.miscTests.TestPanic method) try_and_panic_with_secondary() (toil.test.src.miscTests.TestPanic method) try_path() (in module toil.common) (in module toil.lib.io) tryRun() (toil.batchSystems.mesos.test.ExceptionalThread method) (toil.batchSystems.mesos.test.MesosTestSupport.MesosThread method) (toil.cwl.cwltoil.ExceptionalThread method) (toil.jobStores.utils.ExceptionalThread method) (toil.leader.ScalerThread method) (toil.lib.threading.ExceptionalThread method) (toil.provisioners.clusterScaler.ExceptionalThread method) (toil.provisioners.clusterScaler.ScalerThread method) (toil.test.ApplianceTestSupport.Appliance method) (toil.test.batchSystems.batchSystemTest.MesosTestSupport.MesosThread method) (toil.test.ExceptionalThread method) (toil.test.provisioners.clusterScalerTest.ScalerThread method) (toil.test.sort.sortTest.MesosTestSupport.MesosThread method) (toil.test.src.autoDeploymentTest.ApplianceTestSupport.Appliance method) (toil.test.src.promisedRequirementTest.MesosTestSupport.MesosThread method) typeEmpty() (toil.batchSystems.mesos.batchSystem.JobQueue method) (toil.batchSystems.mesos.JobQueue method)

U

UnexpectedResourceState UnfulfilledPromiseSentinel (class in toil.job) unignoreNode() (toil.batchSystems.abstractBatchSystem.AbstractScalableBatchSystem method) (toil.batchSystems.mesos.batchSystem.AbstractScalableBatchSystem method) (toil.batchSystems.mesos.batchSystem.MesosBatchSystem method) (toil.provisioners.clusterScaler.AbstractScalableBatchSystem method) (toil.test.provisioners.clusterScalerTest.AbstractScalableBatchSystem method) (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method) UnimplementedURLException, [1], [2] unit_name (toil.bus.Names attribute) (toil.job.Names attribute) unix_now_ms() (in module toil.batchSystems.awsBatch) (in module toil.lib.misc) unpack() (toil.common.FileID class method) (toil.cwl.cwltoil.FileID class method) (toil.cwl.utils.FileID class method) (toil.fileStores.abstractFileStore.FileID class method) (toil.fileStores.cachingFileStore.FileID class method) (toil.fileStores.FileID class method) (toil.fileStores.nonCachingFileStore.FileID class method) (toil.job.FileID class method) (toil.jobStores.abstractJobStore.FileID class method) (toil.jobStores.aws.jobStore.FileID class method) (toil.jobStores.fileJobStore.FileID class method) (toil.test.cwl.cwlTest.FileID class method) (toil.test.jobStores.jobStoreTest.FileID class method) (toil.test.src.fileStoreTest.FileID class method) (toil.test.src.importExportFileTest.FileID class method) (toil.test.src.jobFileStoreTest.FileID class method) (toil.wdl.wdltoil.FileID class method) unpack_toil_uri() (in module toil.wdl.wdltoil) unpickle() (toil.batchSystems.abstractBatchSystem.Resource class method) (toil.batchSystems.awsBatch.Resource class method) (toil.batchSystems.contained_executor.Resource class method) (toil.batchSystems.kubernetes.Resource class method) (toil.batchSystems.mesos.executor.Resource class method) (toil.resource.Resource class method) (toil.test.src.resourceTest.Resource class method) UnresolvedDict (class in toil.cwl.cwltoil) unwrap() (in module toil.cwl.cwltoil) (in module toil.job) (in module toil.wdl.wdltoil) unwrap_all() (in module toil.job) (in module toil.wdl.wdltoil) up() (in module toil.test.sort.restart_sort) (in module toil.test.sort.sort) update() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) update_column_widths() (in module toil.utils.toilStats) update_file() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) update_file_stream() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) update_job() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method)

updateClusterSize() (toil.provisioners.clusterScaler.ClusterScaler method) (toil.test.provisioners.clusterScalerTest.ClusterScaler method) UpdatedBatchJobInfo (class in toil.batchSystems.abstractBatchSystem) (class in toil.batchSystems.abstractGridEngineBatchSystem) (class in toil.batchSystems.awsBatch) (class in toil.batchSystems.kubernetes) (class in toil.batchSystems.local_support) (class in toil.batchSystems.mesos.batchSystem) (class in toil.batchSystems.singleMachine) (class in toil.batchSystems.torque) (class in toil.test.batchSystems.batch_system_plugin_test) updateFile() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) updateFileStream() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) updateStaticEC2Instances() (in module toil.lib.ec2nodes) (in module toil.utils.toilUpdateEC2Instances) upload() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo method) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo method) upload_directory() (in module toil.cwl.cwltoil) upload_file() (in module toil.cwl.cwltoil) uploadFile() (in module toil.jobStores.aws.jobStore) (in module toil.jobStores.aws.utils) uploadFromPath() (in module toil.jobStores.aws.jobStore) (in module toil.jobStores.aws.utils) uploadStream() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo method) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo method) UpReturnType (in module toil.cwl.utils) url_exists() (toil.cwl.cwltoil.AbstractJobStore class method) (toil.cwl.utils.AbstractJobStore class method) (toil.fileStores.abstractFileStore.AbstractJobStore class method) (toil.fileStores.cachingFileStore.AbstractJobStore class method) (toil.fileStores.nonCachingFileStore.AbstractJobStore class method) (toil.jobStores.abstractJobStore.AbstractJobStore class method) (toil.jobStores.aws.jobStore.AbstractJobStore class method) (toil.jobStores.fileJobStore.AbstractJobStore class method) (toil.jobStores.googleJobStore.AbstractJobStore class method) (toil.leader.AbstractJobStore class method) (toil.serviceManager.AbstractJobStore class method) (toil.toilState.AbstractJobStore class method) (toil.utils.toilStats.AbstractJobStore class method) (toil.wdl.wdltoil.AbstractJobStore class method) (toil.worker.AbstractJobStore class method) usage_message (in module toil.cwl.cwltoil) useAsync (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) UserDefinedJobArgTypeTest (class in toil.test.src.userDefinedJobArgTypeTest) UserError UserNameAvailableTest (class in toil.test.lib.test_misc) UserNameUnvailableTest (class in toil.test.lib.test_misc) UserNameVeryBrokenTest (class in toil.test.lib.test_misc) userScript (toil.batchSystems.mesos.batchSystem.MesosBatchSystem attribute) utc_now() (in module toil.batchSystems.kubernetes) (in module toil.lib.misc) UtilsTest (class in toil.test.utils.utilsTest) UUID_LENGTH (in module toil.common)

V

VALID_PREFIXES (in module toil.lib.conversions) validDirs (toil.cwl.cwltoil.FileJobStore attribute) (toil.jobStores.fileJobStore.FileJobStore attribute) (toil.test.jobStores.jobStoreTest.FileJobStore attribute) (toil.test.src.workerTest.FileJobStore attribute) (toil.utils.toilDebugFile.FileJobStore attribute) (toil.utils.toilDebugJob.FileJobStore attribute) validDirsSet (toil.cwl.cwltoil.FileJobStore attribute) (toil.jobStores.fileJobStore.FileJobStore attribute) (toil.test.jobStores.jobStoreTest.FileJobStore attribute) (toil.test.src.workerTest.FileJobStore attribute) (toil.utils.toilDebugFile.FileJobStore attribute) (toil.utils.toilDebugJob.FileJobStore attribute) version (in module toil.common) (in module toil.server.app) (in module toil.utils.toilMain) (in module toil.version) (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo property) (toil.test.lib.aws.test_s3.AWSJobStore.FileInfo property)

versionings (toil.jobStores.aws.jobStore.AWSJobStore attribute) (toil.test.lib.aws.test_s3.AWSJobStore attribute) VersionNotImplementedException, [1] VirtualEnvResource (class in toil.resource) virtualize_files() (in module toil.wdl.wdltoil) visit() (toil.cwl.cwltoil.ToilPathMapper method) visit_cwl_class_and_reduce() (in module toil.cwl.cwltoil) (in module toil.cwl.utils) (in module toil.test.cwl.cwlTest) visit_top_cwl_class() (in module toil.cwl.utils) (in module toil.test.cwl.cwlTest) visitSteps() (in module toil.cwl.cwltoil)

W

wait_a_bit() (in module toil.test.src.environmentTest) WAIT_FOR_DEATH_TIMEOUT (in module toil.server.wes.tasks) wait_for_master() (toil.batchSystems.mesos.test.MesosTestSupport method) (toil.test.batchSystems.batchSystemTest.MesosTestSupport method) (toil.test.sort.sortTest.MesosTestSupport method) (toil.test.src.promisedRequirementTest.MesosTestSupport method) wait_instances_running() (in module toil.lib.ec2) (in module toil.provisioners.aws.awsProvisioner) wait_spot_requests_active() (in module toil.lib.ec2) wait_transition() (in module toil.lib.ec2) (in module toil.provisioners.aws.awsProvisioner) wait_until_instance_profile_arn_exists() (in module toil.lib.ec2) (in module toil.provisioners.aws.awsProvisioner) waitForCommit() (toil.batchSystems.abstractBatchSystem.AbstractFileStore method) (toil.cwl.cwltoil.AbstractFileStore method) (toil.cwl.utils.AbstractFileStore method) (toil.fileStores.abstractFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.CachingFileStore method) (toil.fileStores.nonCachingFileStore.AbstractFileStore method) (toil.fileStores.nonCachingFileStore.NonCachingFileStore method) (toil.test.cwl.cwlTest.AbstractFileStore method) (toil.wdl.wdltoil.AbstractFileStore method) (toil.worker.AbstractFileStore method) waitForNode() (toil.provisioners.abstractProvisioner.Node method) (toil.provisioners.aws.awsProvisioner.Node method) (toil.provisioners.gceProvisioner.Node method) (toil.provisioners.node.Node method) (toil.test.provisioners.clusterScalerTest.Node method) wallTime (toil.batchSystems.abstractBatchSystem.UpdatedBatchJobInfo attribute) (toil.batchSystems.abstractGridEngineBatchSystem.UpdatedBatchJobInfo attribute) (toil.batchSystems.awsBatch.UpdatedBatchJobInfo attribute) (toil.batchSystems.kubernetes.UpdatedBatchJobInfo attribute) (toil.batchSystems.local_support.UpdatedBatchJobInfo attribute) (toil.batchSystems.mesos.batchSystem.UpdatedBatchJobInfo attribute) (toil.batchSystems.singleMachine.UpdatedBatchJobInfo attribute) (toil.batchSystems.torque.UpdatedBatchJobInfo attribute) (toil.test.batchSystems.batch_system_plugin_test.UpdatedBatchJobInfo attribute) wdl_dir (toil.test.wdl.wdltoil_test.WDLConformanceTests attribute) wdl_error_reporter() (in module toil.wdl.wdltoil) WDLArrayBindingsJob (class in toil.wdl.wdltoil) WDLBaseJob (class in toil.wdl.wdltoil) WDLBindings (in module toil.wdl.wdltoil) WDLCombineBindingsJob (class in toil.wdl.wdltoil) WDLConditionalJob (class in toil.wdl.wdltoil) WDLConformanceTests (class in toil.test.wdl.wdltoil_test) WDLKubernetesClusterTest (class in toil.test.wdl.wdltoil_test_kubernetes) WDLOutputsJob (class in toil.wdl.wdltoil) WDLRootJob (class in toil.wdl.wdltoil) WDLScatterJob (class in toil.wdl.wdltoil) WDLSectionJob (class in toil.test.wdl.wdltoil_test) (class in toil.wdl.wdltoil) WDLTaskJob (class in toil.wdl.wdltoil) WDLTaskWrapperJob (class in toil.wdl.wdltoil) WDLTests (class in toil.test.wdl.wdltoil_test) WDLWorkflowGraph (class in toil.test.wdl.wdltoil_test) (class in toil.wdl.wdltoil) WDLWorkflowJob (class in toil.wdl.wdltoil) WDLWorkflowNodeJob (class in toil.wdl.wdltoil) WDLWorkflowNodeListJob (class in toil.wdl.wdltoil) WESBackend (class in toil.server.wes.abstract_backend) (class in toil.server.wes.toil_backend) WESClientWithWorkflowEngineParameters (class in toil.server.cli.wes_cwl_runner) which() (in module toil) WIP_SUFFIX (toil.batchSystems.abstractBatchSystem.DeferredFunctionManager attribute) (toil.deferred.DeferredFunctionManager attribute) (toil.worker.DeferredFunctionManager attribute) with_retries() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem method) (toil.batchSystems.gridengine.AbstractGridEngineBatchSystem method) (toil.batchSystems.htcondor.AbstractGridEngineBatchSystem method) (toil.batchSystems.lsf.AbstractGridEngineBatchSystem method) (toil.batchSystems.slurm.AbstractGridEngineBatchSystem method) (toil.batchSystems.torque.AbstractGridEngineBatchSystem method) work_dir (toil.batchSystems.abstractBatchSystem.WorkerCleanupInfo attribute) (toil.batchSystems.cleanup_support.WorkerCleanupInfo attribute) workDir (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) workerCleanup() (toil.batchSystems.abstractBatchSystem.BatchSystemSupport static method) (toil.batchSystems.cleanup_support.BatchSystemSupport static method) (toil.batchSystems.local_support.BatchSystemSupport static method) (toil.batchSystems.mesos.executor.BatchSystemSupport static method) (toil.batchSystems.singleMachine.BatchSystemSupport static method) (toil.test.batchSystems.batchSystemTest.BatchSystemSupport static method) WorkerCleanupContext (class in toil.batchSystems.cleanup_support) WorkerCleanupInfo (class in toil.batchSystems.abstractBatchSystem) (class in toil.batchSystems.cleanup_support) workerScript() (in module toil.utils.toilDebugJob) (in module toil.worker) WorkerTests (class in toil.test.src.workerTest) workflow_debug_jobstore() (in module toil.test.utils.toilDebugTest) workflow_id (toil.batchSystems.abstractBatchSystem.WorkerCleanupInfo attribute) (toil.batchSystems.cleanup_support.WorkerCleanupInfo attribute) workflow_manifest_url_to_path() (in module toil.server.wes.amazon_wes_utils) workflowAttemptNumber (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) WorkflowConflictException, [1] workflowDependencies (toil.server.wes.amazon_wes_utils.FilesDict attribute) WorkflowExecutionException, [1] workflowID (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) workflowInputFiles (toil.server.wes.amazon_wes_utils.FilesDict attribute) WorkflowNotFoundException, [1] workflowOptions (toil.server.wes.amazon_wes_utils.FilesDict attribute) WorkflowPlan (class in toil.server.wes.amazon_wes_utils) workflowSource (toil.server.wes.amazon_wes_utils.FilesDict attribute) WorkflowStateMachine (class in toil.server.utils) (class in toil.server.wes.tasks) (class in toil.server.wes.toil_backend) WorkflowStateStore (class in toil.server.utils) workflowUrl (toil.server.wes.amazon_wes_utils.DataDict attribute) wrapFn() (toil.cwl.cwltoil.Job static method) (toil.fileStores.abstractFileStore.Job static method) (toil.fileStores.cachingFileStore.Job static method) (toil.fileStores.nonCachingFileStore.Job static method) (toil.job.Job static method) (toil.jobStores.aws.jobStore.Job static method) (toil.test.batchSystems.batchSystemTest.Job static method) (toil.test.jobStores.jobStoreTest.Job static method) (toil.test.lib.dockerTest.Job static method) (toil.test.mesos.helloWorld.Job static method) (toil.test.mesos.stress.Job static method) (toil.test.provisioners.restartScript.Job static method) (toil.test.sort.restart_sort.Job static method) (toil.test.sort.sort.Job static method) (toil.test.sort.sortTest.Job static method) (toil.test.src.busTest.Job static method) (toil.test.src.checkpointTest.Job static method) (toil.test.src.deferredFunctionTest.Job static method) (toil.test.src.environmentTest.Job static method) (toil.test.src.fileStoreTest.Job static method) (toil.test.src.helloWorldTest.Job static method) (toil.test.src.importExportFileTest.Job static method) (toil.test.src.jobDescriptionTest.Job static method) (toil.test.src.jobEncapsulationTest.Job static method) (toil.test.src.jobFileStoreTest.Job static method) (toil.test.src.jobServiceTest.Job static method) (toil.test.src.jobTest.Job static method) (toil.test.src.promisedRequirementTest.Job static method) (toil.test.src.promisesTest.Job static method) (toil.test.src.realtimeLoggerTest.Job static method) (toil.test.src.restartDAGTest.Job static method) (toil.test.src.resumabilityTest.Job static method) (toil.test.src.retainTempDirTest.Job static method) (toil.test.src.toilContextManagerTest.Job static method) (toil.test.src.userDefinedJobArgTypeTest.Job static method) (toil.test.utils.utilsTest.Job static method) (toil.utils.toilStats.Job static method) (toil.wdl.wdltoil.Job static method) (toil.worker.Job static method) wrapJobFn() (toil.cwl.cwltoil.Job static method) (toil.fileStores.abstractFileStore.Job static method) (toil.fileStores.cachingFileStore.Job static method) (toil.fileStores.nonCachingFileStore.Job static method) (toil.job.Job static method) (toil.jobStores.aws.jobStore.Job static method) (toil.test.batchSystems.batchSystemTest.Job static method) (toil.test.jobStores.jobStoreTest.Job static method) (toil.test.lib.dockerTest.Job static method) (toil.test.mesos.helloWorld.Job static method) (toil.test.mesos.stress.Job static method) (toil.test.provisioners.restartScript.Job static method) (toil.test.sort.restart_sort.Job static method) (toil.test.sort.sort.Job static method) (toil.test.sort.sortTest.Job static method) (toil.test.src.busTest.Job static method) (toil.test.src.checkpointTest.Job static method) (toil.test.src.deferredFunctionTest.Job static method) (toil.test.src.environmentTest.Job static method) (toil.test.src.fileStoreTest.Job static method) (toil.test.src.helloWorldTest.Job static method) (toil.test.src.importExportFileTest.Job static method) (toil.test.src.jobDescriptionTest.Job static method) (toil.test.src.jobEncapsulationTest.Job static method) (toil.test.src.jobFileStoreTest.Job static method) (toil.test.src.jobServiceTest.Job static method) (toil.test.src.jobTest.Job static method) (toil.test.src.promisedRequirementTest.Job static method) (toil.test.src.promisesTest.Job static method) (toil.test.src.realtimeLoggerTest.Job static method) (toil.test.src.restartDAGTest.Job static method) (toil.test.src.resumabilityTest.Job static method) (toil.test.src.retainTempDirTest.Job static method) (toil.test.src.toilContextManagerTest.Job static method) (toil.test.src.userDefinedJobArgTypeTest.Job static method) (toil.test.utils.utilsTest.Job static method) (toil.utils.toilStats.Job static method) (toil.wdl.wdltoil.Job static method) (toil.worker.Job static method) WritablePipe (class in toil.jobStores.aws.jobStore) (class in toil.jobStores.googleJobStore) (class in toil.jobStores.utils) write() (toil.fileStores.abstractFileStore.WriteWatchingStream method) (toil.jobStores.abstractJobStore.WriteWatchingStream method) (toil.lib.io.WriteWatchingStream method) write_cache() (toil.server.utils.AbstractStateStore method) (toil.server.utils.WorkflowStateStore method) write_config() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) write_file() (in module toil.cwl.cwltoil) (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) write_file_stream() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method)

write_kill_flag() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) write_leader_node_id() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) write_leader_pid() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) write_logs() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) write_messages (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) write_output_files() (toil.server.wes.tasks.ToilWorkflowRunner method) write_scratch_file() (toil.server.wes.tasks.ToilWorkflowRunner method) write_shared_file_stream() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.cwltoil.FileJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AWSJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.FileJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.GoogleJobStore method) (toil.leader.AbstractJobStore method) (toil.provisioners.gceProvisioner.GoogleJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.test.jobStores.jobStoreTest.FileJobStore method) (toil.test.lib.aws.test_s3.AWSJobStore method) (toil.test.src.workerTest.FileJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilDebugFile.FileJobStore method) (toil.utils.toilDebugJob.FileJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) write_temp_file() (in module toil.test.batchSystems.batchSystemTest) write_workflow() (toil.server.wes.tasks.ToilWorkflowRunner method) writeConfig() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) writeFile() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) writeFileStream() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) writeGlobalFile() (toil.batchSystems.abstractBatchSystem.AbstractFileStore method) (toil.cwl.cwltoil.AbstractFileStore method) (toil.cwl.utils.AbstractFileStore method) (toil.fileStores.abstractFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.CachingFileStore method) (toil.fileStores.nonCachingFileStore.AbstractFileStore method) (toil.fileStores.nonCachingFileStore.NonCachingFileStore method) (toil.test.cwl.cwlTest.AbstractFileStore method) (toil.wdl.wdltoil.AbstractFileStore method) (toil.worker.AbstractFileStore method) writeGlobalFileStream() (toil.batchSystems.abstractBatchSystem.AbstractFileStore method) (toil.cwl.cwltoil.AbstractFileStore method) (toil.cwl.utils.AbstractFileStore method) (toil.fileStores.abstractFileStore.AbstractFileStore method) (toil.fileStores.cachingFileStore.AbstractFileStore method) (toil.fileStores.nonCachingFileStore.AbstractFileStore method) (toil.test.cwl.cwlTest.AbstractFileStore method) (toil.wdl.wdltoil.AbstractFileStore method) (toil.worker.AbstractFileStore method) writeGlobalFileWrapper() (in module toil.cwl.cwltoil) writelines() (toil.fileStores.abstractFileStore.WriteWatchingStream method) (toil.jobStores.abstractJobStore.WriteWatchingStream method) (toil.lib.io.WriteWatchingStream method) writeLogFiles() (toil.exceptions.StatsAndLogging class method) (toil.leader.StatsAndLogging class method) (toil.statsAndLogging.StatsAndLogging class method) (toil.test.jobStores.jobStoreTest.StatsAndLogging class method) (toil.utils.toilStatus.StatsAndLogging class method) writeLogs (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) writeLogsFromAllJobs (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) writeLogsGzip (toil.batchSystems.abstractBatchSystem.Config attribute) (toil.batchSystems.awsBatch.Config attribute) (toil.batchSystems.cleanup_support.Config attribute) (toil.batchSystems.kubernetes.Config attribute) (toil.batchSystems.local_support.Config attribute) (toil.batchSystems.singleMachine.Config attribute) (toil.common.Config attribute) (toil.job.Config attribute) (toil.jobStores.abstractJobStore.Config attribute) (toil.leader.Config attribute) (toil.provisioners.clusterScaler.Config attribute) (toil.test.batchSystems.batchSystemTest.Config attribute) (toil.test.batchSystems.test_slurm.Config attribute) (toil.test.jobStores.jobStoreTest.Config attribute) (toil.test.provisioners.clusterScalerTest.Config attribute) (toil.test.src.workerTest.Config attribute) (toil.test.utils.utilsTest.Config attribute) (toil.utils.toilDebugFile.Config attribute) (toil.utils.toilDebugJob.Config attribute) (toil.utils.toilKill.Config attribute) (toil.utils.toilStats.Config attribute) (toil.utils.toilStatus.Config attribute) (toil.worker.Config attribute) writeSharedFileStream() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) writeStatsAndLogging() (toil.cwl.cwltoil.AbstractJobStore method) (toil.cwl.utils.AbstractJobStore method) (toil.fileStores.abstractFileStore.AbstractJobStore method) (toil.fileStores.cachingFileStore.AbstractJobStore method) (toil.fileStores.nonCachingFileStore.AbstractJobStore method) (toil.jobStores.abstractJobStore.AbstractJobStore method) (toil.jobStores.aws.jobStore.AbstractJobStore method) (toil.jobStores.fileJobStore.AbstractJobStore method) (toil.jobStores.googleJobStore.AbstractJobStore method) (toil.leader.AbstractJobStore method) (toil.serviceManager.AbstractJobStore method) (toil.toilState.AbstractJobStore method) (toil.utils.toilStats.AbstractJobStore method) (toil.wdl.wdltoil.AbstractJobStore method) (toil.worker.AbstractJobStore method) writeTo() (toil.jobStores.aws.jobStore.ReadablePipe method) (toil.jobStores.aws.jobStore.ReadableTransformingPipe method) (toil.jobStores.googleJobStore.ReadablePipe method) (toil.jobStores.utils.ReadablePipe method) (toil.jobStores.utils.ReadableTransformingPipe method) writeToAppliance() (toil.test.ApplianceTestSupport.Appliance method) (toil.test.src.autoDeploymentTest.ApplianceTestSupport.Appliance method) WriteWatchingStream (class in toil.fileStores.abstractFileStore) (class in toil.jobStores.abstractJobStore) (class in toil.lib.io)

Z

zone_to_region() (in module toil.lib.aws) (in module toil.provisioners.aws.awsProvisioner) (in module toil.test.provisioners.clusterTest)

ZoneTuple (in module toil.provisioners.aws)