Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
Z
_
__call__() (toil.batchSystems.options.OptionSetter method)
(toil.lib.objects.InnerClass method)
(toil.lib.throttle.LocalThrottle method)
(toil.lib.throttle.throttle method)
__copy__() (toil.job.Requirer method)
__deepcopy__() (toil.job.Requirer method)
__del__() (toil.deferred.DeferredFunctionManager method)
(toil.fileStores.cachingFileStore.CachingFileStore method)
(toil.fileStores.nonCachingFileStore.NonCachingFileStore method)
__enter__() (toil.batchSystems.cleanup_support.WorkerCleanupContext method)
(toil.common.Toil method)
(toil.jobStores.utils.ReadablePipe method)
(toil.jobStores.utils.WritablePipe method)
(toil.lib.exceptions.panic method)
(toil.lib.throttle.throttle method)
(toil.realtimeLogger.RealtimeLogger method)
(toil.test.ApplianceTestSupport.Appliance method)
__eq__() (toil.batchSystems.mesos.Shape method)
(toil.common.Config method)
(toil.job.TemporaryID method)
(toil.lib.ec2nodes.InstanceType method)
(toil.provisioners.abstractProvisioner.Shape method)
(toil.wdl.wdl_types.WDLPair method)
(toil.wdl.wdl_types.WDLType method)
__exit__() (toil.batchSystems.cleanup_support.WorkerCleanupContext method)
(toil.common.Toil method)
(toil.jobStores.utils.ReadablePipe method)
(toil.jobStores.utils.WritablePipe method)
(toil.lib.exceptions.panic method)
(toil.lib.throttle.throttle method)
(toil.realtimeLogger.RealtimeLogger method)
(toil.test.ApplianceTestSupport.Appliance method)
__get__() (toil.lib.objects.InnerClass method)
__getattr__() (toil.batchSystems.kubernetes.KubernetesBatchSystem.DecoratorWrapper method)
(toil.realtimeLogger.RealtimeLoggerMetaclass method)
__getattribute__() (toil.lib.expando.MagicExpando method)
__getstate__() (toil.job.Requirer method)
__gt__() (toil.batchSystems.mesos.MesosShape method)
(toil.batchSystems.mesos.Shape method)
(toil.provisioners.abstractProvisioner.Shape method)
__hash__() (toil.batchSystems.mesos.Shape method)
(toil.common.Config method)
(toil.job.TemporaryID method)
(toil.provisioners.abstractProvisioner.Shape method)
(toil.provisioners.node.Node method)
__iter__() (toil.lib.iterables.concat method)
(toil.test.concat method)
__ne__() (toil.job.TemporaryID method)
__reduce__() (toil.job.EncapsulatedJob method)
(toil.job.Promise method)
__repr__ (toil.deferred.DeferredFunction attribute)
__repr__() (toil.batchSystems.abstractBatchSystem.ResourcePool method)
(toil.batchSystems.abstractBatchSystem.ResourceSet method)
(toil.batchSystems.mesos.Shape method)
(toil.bus.JobStatus method)
(toil.cwl.cwltoil.ResolveSource method)
(toil.job.JobDescription method)
(toil.job.TemporaryID method)
(toil.jobStores.aws.jobStore.AWSJobStore.FileInfo method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.provisioners.abstractProvisioner.Shape method)
(toil.provisioners.node.Node method)
(toil.wdl.wdl_types.WDLPair method)
(toil.wdl.wdl_types.WDLType method)
__setstate__() (toil.job.UnfulfilledPromiseSentinel static method)
__slots__ (toil.lib.ec2nodes.InstanceType attribute)
__str__() (toil.batchSystems.abstractBatchSystem.InsufficientSystemResources method)
(toil.batchSystems.abstractBatchSystem.ResourcePool method)
(toil.batchSystems.abstractBatchSystem.ResourceSet method)
(toil.batchSystems.DeadlockException method)
(toil.batchSystems.mesos.Shape method)
(toil.cwl.cwltoil.ToilTool method)
(toil.deferred.DeferredFunction method)
(toil.exceptions.FailedJobsException method)
(toil.job.Job method)
(toil.job.JobDescription method)
(toil.job.TemporaryID method)
(toil.lib.ec2nodes.InstanceType method)
(toil.lib.misc.CalledProcessErrorStderr method)
(toil.provisioners.abstractProvisioner.Shape method)
(toil.provisioners.clusterScaler.JobTooBigError method)
(toil.provisioners.clusterScaler.NodeReservation method)
(toil.provisioners.node.Node method)
(toil.wdl.wdl_types.WDLType method)
A
A (in module tutorial_encapsulation)
(in module tutorial_encapsulation2)
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.node)
abspath_file() (in module toil.wdl.wdl_functions)
abspath_single_file() (in module toil.wdl.wdl_functions)
AbstractAWSAutoscaleTest (class in toil.test.provisioners.aws.awsProvisionerTest)
AbstractBatchSystem (class in toil.batchSystems.abstractBatchSystem)
AbstractClusterTest (class in toil.test.provisioners.clusterTest)
AbstractEncryptedJobStoreTest (class in toil.test.jobStores.jobStoreTest)
AbstractEncryptedJobStoreTest.Test (class in toil.test.jobStores.jobStoreTest)
AbstractFileStore (class in toil.fileStores.abstractFileStore)
AbstractGCEAutoscaleTest (class in toil.test.provisioners.gceProvisionerTest)
AbstractGridEngineBatchSystem (class in toil.batchSystems.abstractGridEngineBatchSystem)
AbstractGridEngineBatchSystem.Worker (class in toil.batchSystems.abstractGridEngineBatchSystem)
AbstractJobStore (class in toil.jobStores.abstractJobStore)
AbstractJobStoreTest (class in toil.test.jobStores.jobStoreTest)
AbstractJobStoreTest.Test (class in toil.test.jobStores.jobStoreTest)
AbstractProvisioner (class in toil.provisioners.abstractProvisioner)
AbstractProvisioner.InstanceConfiguration (class in toil.provisioners.abstractProvisioner)
AbstractScalableBatchSystem (class in toil.batchSystems.abstractBatchSystem)
AbstractStateStore (class in toil.server.utils)
AbstractToilWESServerTest (class in toil.test.server.serverTest)
accelerator_satisfies() (in module toil.job)
AcceleratorRequirement (class in toil.job)
accelerators (toil.job.Job property)
(toil.job.RequirementsDict attribute)
(toil.job.Requirer property)
accelerators_fully_satisfy() (in module toil.job)
acquire() (toil.batchSystems.abstractBatchSystem.ResourcePool method)
(toil.batchSystems.abstractBatchSystem.ResourceSet method)
acquireNow() (toil.batchSystems.abstractBatchSystem.ResourcePool method)
(toil.batchSystems.abstractBatchSystem.ResourceSet method)
acquisitionOf() (toil.batchSystems.abstractBatchSystem.ResourcePool method)
(toil.batchSystems.abstractBatchSystem.ResourceSet method)
AcquisitionTimeoutException
add_all_batchsystem_options() (in module toil.batchSystems.options)
add_logging_options() (in module toil.statsAndLogging)
add_options() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem class method)
(toil.batchSystems.awsBatch.AWSBatchBatchSystem class method)
(toil.batchSystems.kubernetes.KubernetesBatchSystem class method)
(toil.batchSystems.mesos.batchSystem.MesosBatchSystem class method)
(toil.batchSystems.parasol.ParasolBatchSystem class method)
(toil.batchSystems.singleMachine.SingleMachineBatchSystem class method)
(toil.batchSystems.slurm.SlurmBatchSystem class method)
(toil.batchSystems.tes.TESBatchSystem class method)
add_prometheus_data_source() (toil.common.ToilMetrics method)
add_provisioner_options() (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.provisioners.abstractProvisioner.AbstractProvisioner method)
addBatchSystemFactory() (in module toil.batchSystems.registry)
addChild() (toil.cwl.cwltoil.SelfJob method)
(toil.job.EncapsulatedJob method)
(toil.job.Job method)
(toil.job.JobDescription method)
(toil.job.ServiceHostJob method)
addChildFn() (toil.job.Job method)
addChildJobFn() (toil.job.Job method)
addCompletedJob() (toil.provisioners.clusterScaler.ClusterScaler method)
(toil.provisioners.clusterScaler.ScalerThread method)
addFile() (toil.provisioners.abstractProvisioner.AbstractProvisioner.InstanceConfiguration method)
addFollowOn() (toil.job.EncapsulatedJob method)
(toil.job.Job method)
(toil.job.JobDescription method)
(toil.job.ServiceHostJob method)
addFollowOnFn() (toil.job.Job method)
addFollowOnJobFn() (toil.job.Job method)
addJob() (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method)
addJobShape() (toil.provisioners.clusterScaler.BinPackedFit method)
addKubernetesLeader() (toil.provisioners.abstractProvisioner.AbstractProvisioner method)
addKubernetesServices() (toil.provisioners.abstractProvisioner.AbstractProvisioner method)
addKubernetesWorker() (toil.provisioners.abstractProvisioner.AbstractProvisioner method)
addManagedNodes() (toil.provisioners.abstractProvisioner.AbstractProvisioner method)
(toil.provisioners.aws.awsProvisioner.AWSProvisioner method)
addNodeExporterService() (toil.provisioners.abstractProvisioner.AbstractProvisioner method)
addNodes() (toil.provisioners.abstractProvisioner.AbstractProvisioner method)
(toil.provisioners.aws.awsProvisioner.AWSProvisioner method)
(toil.provisioners.gceProvisioner.GCEProvisioner method)
(toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method)
addOptions() (in module toil.common)
addPredecessor() (toil.job.JobDescription method)
addRandomFollowOnEdges() (toil.test.src.jobTest.JobTest method)
addService() (toil.job.EncapsulatedJob method)
(toil.job.Job method)
(toil.job.ServiceHostJob method)
addServiceHostJob() (toil.job.JobDescription method)
addSSHRSAKey() (toil.provisioners.abstractProvisioner.AbstractProvisioner.InstanceConfiguration method)
addToilOptions() (toil.job.Job.Runner static method)
addUnit() (toil.provisioners.abstractProvisioner.AbstractProvisioner.InstanceConfiguration method)
addVolumesService() (toil.provisioners.abstractProvisioner.AbstractProvisioner method)
adjustCacheLimit() (toil.fileStores.cachingFileStore.CachingFileStore method)
adjustEndingReservationForJob() (in module toil.provisioners.clusterScaler)
align (in module tutorial_docker)
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.job.JobDescription method)
AlwaysFail (class in toil.test.src.checkpointTest)
AMITest (class in toil.test.lib.test_ec2)
analysisJob() (in module tutorial_requirements)
analyze() (toil.wdl.versions.dev.AnalyzeDevelopmentWDL method)
(toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
(toil.wdl.versions.v1.AnalyzeV1WDL method)
(toil.wdl.wdl_analysis.AnalyzeWDL method)
AnalyzeDevelopmentWDL (class in toil.wdl.versions.dev)
AnalyzeDraft2WDL (class in toil.wdl.versions.draft2)
AnalyzeV1WDL (class in toil.wdl.versions.v1)
AnalyzeWDL (class in toil.wdl.wdl_analysis)
annotation_name (toil.bus.JobAnnotationMessage attribute)
annotation_value (toil.bus.JobAnnotationMessage attribute)
annotations (toil.bus.JobStatus attribute)
api (toil.job.AcceleratorRequirement attribute)
apiDockerCall() (in module toil.lib.docker)
ApplianceImageNotFound
,
[1]
applianceSelf() (in module toil)
(in module toil.test)
ApplianceTestSupport (class in toil.test)
ApplianceTestSupport.Appliance (class in toil.test)
ApplianceTestSupport.LeaderThread (class in toil.test)
ApplianceTestSupport.WorkerThread (class in toil.test)
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)
args (in module fake_mpi_run)
as_map() (in module toil.wdl.wdl_functions)
as_pairs() (in module toil.wdl.wdl_functions)
assertIsCopy() (toil.test.src.userDefinedJobArgTypeTest.Foo method)
assertUrl() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method)
assign_job_id() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
assignConfig() (toil.job.Job method)
(toil.job.Requirer method)
assignID() (toil.jobStores.abstractJobStore.AbstractJobStore method)
atomic_copy() (in module toil.lib.io)
atomic_copyobj() (in module toil.lib.io)
atomic_install() (in module toil.lib.io)
atomic_tmp_file() (in module toil.lib.io)
AtomicFileCreate() (in module toil.lib.io)
attemptToAddJob() (toil.provisioners.clusterScaler.NodeReservation method)
attributesToBinary() (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_marketplace_flatcar_ami_search() (in module toil.lib.aws.ami)
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)
awsFilterImpairedNodes() (in module toil.provisioners.aws.awsProvisioner)
AWSJobStore (class in toil.jobStores.aws.jobStore)
AWSJobStore.FileInfo (class in toil.jobStores.aws.jobStore)
AWSJobStoreTest (class in toil.test.jobStores.jobStoreTest)
AWSManagedAutoscaleTest (class in toil.test.provisioners.aws.awsProvisionerTest)
AWSProvisioner (class in toil.provisioners.aws.awsProvisioner)
AWSProvisionerBenchTest (class in toil.test.provisioners.aws.awsProvisionerTest)
awsRegion() (toil.test.ToilTest class method)
AWSRestartTest (class in toil.test.provisioners.aws.awsProvisionerTest)
awsRetry() (in module toil.provisioners.aws.awsProvisioner)
awsRetryPredicate() (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)
b_to_mib() (in module toil.lib.conversions)
badChild() (in module toil.test.src.resumabilityTest)
basename() (in module toil.wdl.wdl_functions)
BaseToilWdlTest (class in toil.test.wdl.toilwdlTest)
baseVersion (in module toil.version)
batch() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
batch_logs_dir (toil.common.Config attribute)
batch_system (toil.bus.ExternalBatchIdMessage attribute)
(toil.bus.JobStatus attribute)
BATCH_SYSTEM_FACTORY_REGISTRY (in module toil.batchSystems.registry)
BATCH_SYSTEMS (in module toil.batchSystems.registry)
BatchJobExitReason (class in toil.batchSystems.abstractBatchSystem)
batchSystem (toil.common.Config attribute)
BatchSystemCleanupSupport (class in toil.batchSystems.cleanup_support)
BatchSystemLocalSupport (class in toil.batchSystems.local_support)
BatchSystemPluginTest (class in toil.test.batchSystems.batchSystemTest)
BatchSystemSupport (class in toil.batchSystems.abstractBatchSystem)
belongsToToil (toil.resource.ModuleDescriptor property)
BINARY_PREFIXES (in module toil.lib.conversions)
binaryStringFn() (in module tutorial_dynamic)
binaryStrings() (in module tutorial_promises2)
binaryToAttributes() (toil.jobStores.aws.utils.SDBHelper class method)
binPack() (toil.provisioners.clusterScaler.BinPackedFit method)
BinPackedFit (class in toil.provisioners.clusterScaler)
binPacking() (in module toil.provisioners.clusterScaler)
BinPackingTest (class in toil.test.provisioners.clusterScalerTest)
boto2() (toil.lib.aws.session.AWSConnectionManager method)
boto3_session (in module toil.jobStores.aws.jobStore)
botocore (in module toil.lib.retry)
BotoServerError (in module toil.lib.aws.utils)
brand (toil.job.AcceleratorRequirement attribute)
broken_job() (in module debugWorkflow)
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)
BucketUsingTest (class in toil.test.server.serverTest)
BUFFER_SIZE (toil.jobStores.fileJobStore.FileJobStore attribute)
build_tag_dict_from_env() (in module toil.lib.aws)
build_wes_request() (toil.server.cli.wes_cwl_runner.WESClientWithWorkflowEngineParameters method)
buildElement() (in module toil.utils.toilStats)
buildLocator() (toil.common.Toil static method)
bytes2human() (in module toil.lib.conversions)
(in module toil.lib.humanize)
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.common)
CachedUnpicklingJobStoreTest (class in toil.test.src.promisesTest)
CacheError
cacheTag (in module toil.version)
CacheUnbalancedError
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)
call_cmd() (toil.server.wes.tasks.ToilWorkflowRunner method)
call_command() (in module toil.lib.misc)
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
can_fake_root() (toil.wdl.wdltoil.WDLTaskJob method)
cancel() (toil.server.wes.tasks.MultiprocessingTaskRunner class method)
(toil.server.wes.tasks.TaskRunner static method)
cancel_run() (in module toil.server.wes.tasks)
(toil.server.wes.abstract_backend.WESBackend method)
(toil.server.wes.toil_backend.ToilBackend method)
category_choices (in module toil.utils.toilStats)
ceil() (in module toil.wdl.wdl_functions)
celery (in module toil.server.celery_app)
cgcloudVersion (in module toil.version)
ChainedIndexedPromisesTest (class in toil.test.src.promisesTest)
check() (toil.bus.MessageBus method)
(toil.job.Job.Service method)
(toil.provisioners.clusterScaler.ScalerThread method)
(toil.serviceManager.ServiceManager method)
(toil.statsAndLogging.StatsAndLogging method)
(toil.test.batchSystems.batchSystemTest.Service method)
(toil.test.src.jobServiceTest.ToySerializableService method)
(toil.test.src.jobServiceTest.ToyService method)
(toil.test.src.jobTest.TrivialService method)
(tutorial_services.DemoService method)
check_cwltool_version() (in module toil.cwl)
check_directory_dict_invariants() (in module toil.cwl.cwltoil)
check_for_coordination_corruption() (toil.fileStores.nonCachingFileStore.NonCachingFileStore static method)
check_for_state_corruption() (toil.fileStores.nonCachingFileStore.NonCachingFileStore method)
check_function() (toil.test.wdl.builtinTest.WdlWorkflowsTest method)
check_lsf_json_output_supported() (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.singleMachine.SingleMachineBatchSystem method)
check_status() (toil.test.utils.utilsTest.UtilsTest method)
check_valid_node_types() (in module toil.provisioners)
checkDockerImageExists() (in module toil)
checkDockerSchema() (in module toil)
checkExitCode() (toil.test.docs.scriptsTest.ToilDocumentationTest method)
checkExpectedOut() (toil.test.docs.scriptsTest.ToilDocumentationTest method)
checkExpectedPattern() (toil.test.docs.scriptsTest.ToilDocumentationTest method)
checkForDeadlocks() (toil.leader.Leader method)
checkJobGraphAcylic() (toil.job.Job method)
checkJobGraphConnected() (toil.job.Job method)
checkJobGraphForDeadlocks() (toil.job.Job method)
checkNewCheckpointsAreLeafVertices() (toil.job.Job method)
checkOnJobs() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.Worker method)
checkpoint (toil.job.Job property)
CheckpointFailsFirstTime (class in toil.test.src.checkpointTest)
CheckpointJobDescription (class in toil.job)
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)
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.jobStores.abstractJobStore.AbstractJobStore method)
clean_up() (toil.server.wes.toil_backend.ToilWorkflow method)
clean_work_dir (toil.batchSystems.abstractBatchSystem.WorkerCleanupInfo attribute)
cleanCommand (toil.test.utils.utilsTest.UtilsTest property)
cleanJobStoreUtil() (toil.test.provisioners.gceProvisionerTest.AbstractGCEAutoscaleTest method)
cleanSystem() (toil.resource.Resource class method)
cleanUpExternalStores() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test class method)
cleanupWorker() (toil.deferred.DeferredFunctionManager class method)
cleanWorkDir (toil.common.Config attribute)
CleanWorkDirTest (class in toil.test.src.retainTempDirTest)
clear_dependents() (toil.job.JobDescription method)
clear_nonexistent_dependents() (toil.job.JobDescription method)
clearRemainingTryCount() (toil.job.JobDescription method)
client() (in module toil.lib.aws.session)
(toil.lib.aws.session.AWSConnectionManager method)
close() (toil.lib.io.WriteWatchingStream method)
cloud (toil.provisioners.abstractProvisioner.AbstractProvisioner attribute)
cluster_factory() (in module toil.provisioners)
CLUSTER_LAUNCHING_PERMISSIONS (in module toil.lib.aws.iam)
ClusterCombinationNotSupportedException
ClusterDesiredSizeMessage (class in toil.bus)
ClusterScaler (class in toil.provisioners.clusterScaler)
ClusterScalerTest (class in toil.test.provisioners.clusterScalerTest)
ClusterSizeMessage (class in toil.bus)
ClusterStats (class in toil.provisioners.clusterScaler)
ClusterTypeNotSupportedException
coalesce_job_exit_codes() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.Worker method)
(toil.batchSystems.lsf.LSFBatchSystem.Worker method)
(toil.batchSystems.slurm.SlurmBatchSystem.Worker method)
collect_attachments() (toil.server.wes.abstract_backend.WESBackend method)
collect_by_key() (in module toil.wdl.wdl_functions)
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)
(in module toil.test.wdl.conftest)
collect_policy_actions() (in module toil.lib.aws.iam)
collect_process_name_garbage() (in module toil.lib.threading)
ColumnWidths (class in toil.utils.toilStats)
combine_bindings() (in module toil.wdl.wdltoil)
combine_dicts() (in module toil.wdl.wdl_functions)
commit_job() (toil.toilState.ToilState method)
compare_runs() (in module toil.test.wdl.toilwdlTest)
compare_vcf_files() (in module toil.test.wdl.toilwdlTest)
compat_bytes() (in module toil.lib.compatibility)
compat_bytes_recursive() (in module toil.lib.compatibility)
compound_types (toil.wdl.wdl_analysis.AnalyzeWDL attribute)
computeColumnWidths() (in module toil.utils.toilStats)
concat (class in toil.lib.iterables)
(class in toil.test)
ConcurrentFileModificationException
Conditional (class in toil.cwl.cwltoil)
Config (class in toil.common)
config (toil.common.Toil attribute)
(toil.jobStores.abstractJobStore.AbstractJobStore property)
configure_root_logger() (in module toil.statsAndLogging)
ConflictingPredecessorError
CONFORMANCE_TEST_TIMEOUT (in module toil.test.cwl.cwlTest)
connect() (toil.bus.MessageBus method)
connect_output_file() (toil.bus.MessageBus method)
connect_to_state_store() (in module toil.server.utils)
connect_to_workflow_state_store() (in module toil.server.utils)
connection_reset() (in module toil.lib.aws.utils)
connectSchedd() (toil.batchSystems.htcondor.HTCondorBatchSystem.Worker method)
CONSISTENCY_TICKS (in module toil.jobStores.aws.jobStore)
CONSISTENCY_TIME (in module toil.jobStores.aws.jobStore)
containerIsRunning() (in module toil.lib.docker)
content (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo property)
ConversionTest (class in toil.test.lib.test_conversions)
convert_units() (in module toil.lib.conversions)
convertPromises() (toil.job.PromisedRequirement static method)
coordination_dir (toil.batchSystems.abstractBatchSystem.WorkerCleanupInfo attribute)
copy() (toil.lib.expando.Expando method)
copyFrom() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo method)
copyKeyMultipart() (in module toil.jobStores.aws.utils)
copySshKeys() (toil.provisioners.node.Node method)
copySubRangeOfFile() (in module toil.test.sort.restart_sort)
(in module toil.test.sort.sort)
copyTo() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo method)
coreRsync() (toil.provisioners.node.Node method)
cores (toil.job.Job property)
(toil.job.RequirementsDict attribute)
(toil.job.Requirer property)
coreSSH() (toil.provisioners.node.Node method)
count (toil.job.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.toilState.ToilState method)
CovItemT (toil.batchSystems.kubernetes.KubernetesBatchSystem attribute)
cpu_count() (in module toil.batchSystems.mesos.test)
(in module toil.lib.threading)
(in module toil.test)
cpuCount (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemJobTest attribute)
create() (toil.deferred.DeferredFunction class method)
(toil.job.PromisedRequirementFunctionWrappingJob class method)
(toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore.FileInfo class method)
(toil.resource.Resource class method)
(toil.wdl.wdl_types.WDLType method)
create_app() (in module toil.server.app)
create_auto_scaling_group() (in module toil.lib.ec2)
create_celery_app() (in module toil.server.celery_app)
create_client() (toil.jobStores.googleJobStore.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)
create_job() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
create_launch_template() (in module toil.lib.ec2)
create_ondemand_instances() (in module toil.lib.ec2)
create_root_job() (toil.jobStores.abstractJobStore.AbstractJobStore method)
create_s3_bucket() (in module toil.lib.aws.utils)
create_spot_instances() (in module toil.lib.ec2)
create_status_sentinel_file() (toil.leader.Leader method)
create_subgraph() (toil.wdl.wdltoil.WDLSectionJob method)
create_tags_dict() (in module toil.utils.toilLaunchCluster)
create_tasks_dict() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
create_wdl_compound_type() (toil.wdl.wdl_analysis.AnalyzeWDL method)
create_wdl_primitive_type() (toil.wdl.wdl_analysis.AnalyzeWDL method)
create_workflows_dict() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
createBatchSystem() (toil.common.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.ParasolBatchSystemTest method)
(toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystemTest method)
(toil.test.batchSystems.batchSystemTest.SlurmBatchSystemTest method)
(toil.test.batchSystems.batchSystemTest.TESBatchSystemTest method)
(toil.test.batchSystems.batchSystemTest.TorqueBatchSystemTest method)
createClusterSettings() (toil.provisioners.abstractProvisioner.AbstractProvisioner method)
(toil.provisioners.aws.awsProvisioner.AWSProvisioner method)
(toil.provisioners.gceProvisioner.GCEProvisioner method)
(toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method)
createClusterUtil() (toil.test.provisioners.clusterTest.AbstractClusterTest method)
(toil.test.provisioners.gceProvisionerTest.AbstractGCEAutoscaleTest method)
createConfig() (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemTest class method)
(toil.test.batchSystems.batchSystemTest.MesosBatchSystemTest class method)
createFileStore() (toil.fileStores.abstractFileStore.AbstractFileStore static method)
createJobs() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.Worker method)
(toil.batchSystems.htcondor.HTCondorBatchSystem.Worker method)
createRootJob() (toil.jobStores.abstractJobStore.AbstractJobStore method)
createSummary() (in module toil.utils.toilStats)
cross() (in module toil.wdl.wdl_functions)
current_process_name_for (in module toil.lib.threading)
current_process_name_lock (in module toil.lib.threading)
current_size (toil.bus.ClusterSizeMessage attribute)
currentCommit (in module toil)
(in module toil.version)
custom_repr (in module toil.jobStores.aws.jobStore)
customDockerInitCmd() (in module toil)
customInitCmd() (in module toil)
CWL_UNSUPPORTED_REQUIREMENT_EXCEPTION (in module toil.cwl.utils)
CWL_UNSUPPORTED_REQUIREMENT_EXIT_CODE (in module toil.cwl.utils)
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.cwl.cwlTest)
CWLScatter (class in toil.cwl.cwltoil)
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.singleMachine.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)
dbFn() (in module tutorial_services)
DeadlockException
debugWorkflow
module
DECIMAL_PREFIXES (in module toil.lib.conversions)
decode_directory() (in module toil.cwl.cwltoil)
decorateSubHeader() (in module toil.utils.toilStats)
decorateTitle() (in module toil.utils.toilStats)
decrypt() (in module toil.lib.encryption._dummy)
(in module toil.lib.encryption._nacl)
default() (toil.wdl.wdl_functions.WDLJSONEncoder method)
DEFAULT_BATCH_SYSTEM (in module toil.batchSystems.registry)
default_caching() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
DEFAULT_DELAYS (in module toil.lib.retry)
DEFAULT_LOGLEVEL (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.lib.retry)
DEFAULT_TMPDIR (in module toil.cwl.cwltoil)
DEFAULT_TMPDIR_PREFIX (in module toil.cwl.cwltoil)
default_value (toil.wdl.wdl_types.WDLFileType property)
(toil.wdl.wdl_types.WDLStringType property)
(toil.wdl.wdl_types.WDLType property)
defaultLevel (toil.realtimeLogger.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)
defaultN (in module toil.test.sort.sortTest)
defaultRequirements (in module toil.test.batchSystems.batchSystemTest)
defaultTargetTime (in module toil.common)
DefaultWithSource (class in toil.cwl.cwltoil)
defer() (toil.job.Job method)
DeferredFunction (class in toil.deferred)
DeferredFunctionManager (class in toil.deferred)
DeferredFunctionTest (class in toil.test.src.deferredFunctionTest)
defined() (in module toil.wdl.wdl_functions)
delete() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore.FileInfo method)
delete_file() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
delete_iam_instance_profile() (in module toil.lib.aws.utils)
delete_iam_role() (in module toil.lib.aws.utils)
delete_job() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
(toil.toilState.ToilState method)
delete_s3_bucket() (in module toil.lib.aws.utils)
delete_sdb_domain() (in module toil.lib.aws.utils)
deleteFile() (toil.jobStores.abstractJobStore.AbstractJobStore method)
deleteGlobalFile() (toil.fileStores.abstractFileStore.AbstractFileStore method)
(toil.fileStores.cachingFileStore.CachingFileStore method)
(toil.fileStores.nonCachingFileStore.NonCachingFileStore method)
deleteLocalFile() (toil.fileStores.abstractFileStore.AbstractFileStore method)
(toil.fileStores.cachingFileStore.CachingFileStore method)
(toil.fileStores.nonCachingFileStore.NonCachingFileStore method)
DemoService (class in tutorial_services)
deployScript() (toil.test.ApplianceTestSupport.Appliance method)
deprecated() (in module toil.lib.compatibility)
description (toil.job.Job property)
desired_labels (toil.batchSystems.kubernetes.KubernetesBatchSystem.Placement attribute)
desired_size (toil.bus.ClusterDesiredSizeMessage attribute)
destroy() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
destroy_all_process_names() (in module toil.lib.threading)
destroyCluster() (toil.provisioners.abstractProvisioner.AbstractProvisioner method)
(toil.provisioners.aws.awsProvisioner.AWSProvisioner method)
(toil.provisioners.gceProvisioner.GCEProvisioner method)
(toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method)
(toil.test.provisioners.clusterTest.AbstractClusterTest method)
destroyClusterUtil() (toil.test.provisioners.gceProvisionerTest.AbstractGCEAutoscaleTest method)
determine_load_listing() (in module toil.cwl.cwltoil)
devirtualize_files() (in module toil.wdl.wdltoil)
DIAL_SPECIFIC_REGION_CONFIG (in module toil.jobStores.aws.utils)
diamond() (in module toil.test.src.jobTest)
dict_from_JSON() (in module toil.wdl.utils)
DirectoryContents (in module toil.cwl.cwltoil)
DirectoryResource (class in toil.resource)
DirectoryStructure (in module toil.cwl.utils)
dirname (in module toil.lib.ec2nodes)
dirPath (toil.resource.ModuleDescriptor attribute)
dirty (in module toil.version)
disableAutoDeployment (toil.common.Config attribute)
disconnected() (toil.batchSystems.mesos.executor.MesosExecutor method)
discoverFiles (class in tutorial_discoverfiles)
disk (toil.job.Job property)
(toil.job.RequirementsDict attribute)
(toil.job.Requirer property)
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)
dockerName (in module toil.version)
dockerRegistry (in module toil.version)
dockerStop() (in module toil.lib.docker)
dockerTag (in module toil.version)
DockerTest (class in toil.test.lib.dockerTest)
down() (in module toil.test.sort.restart_sort)
(in module toil.test.sort.sort)
download() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo method)
(toil.resource.Resource method)
(toil.test.cwl.cwlTest.CWLWorkflowTest method)
download_directory() (toil.test.cwl.cwlTest.CWLWorkflowTest method)
download_file_from_internet() (in module toil.server.utils)
download_file_from_s3() (in module toil.server.utils)
download_structure() (in module toil.cwl.utils)
download_subdirectory() (toil.test.cwl.cwlTest.CWLWorkflowTest method)
downloadStream() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo method)
DownReturnType (in module toil.cwl.utils)
drop_missing_files() (in module toil.wdl.wdltoil)
duplicate_quotes() (toil.batchSystems.htcondor.HTCondorBatchSystem.Worker method)
E
e() (in module toil.test.src.promisesTest)
E2Instances (in module toil.lib.generatedEC2Lists)
ec2InstancesByRegion (in module toil.lib.generatedEC2Lists)
EC2Regions (in module toil.lib.ec2nodes)
emit() (toil.test.src.realtimeLoggerTest.MessageDetector method)
empty() (toil.bus.MessageInbox method)
enable_public_objects() (in module toil.lib.aws.utils)
encapsulate() (toil.job.Job method)
EncapsulatedJob (class in toil.job)
encapsulatedJobFn() (in module toil.test.src.jobEncapsulationTest)
encode_data (toil.test.wdl.toilwdlTest.ToilWdlIntegrationTest attribute)
encode_data_dir (toil.test.wdl.toilwdlTest.ToilWdlIntegrationTest attribute)
encode_directory() (in module toil.cwl.cwltoil)
encrypt() (in module toil.lib.encryption._dummy)
(in module toil.lib.encryption._nacl)
EncryptedAWSJobStoreTest (class in toil.test.jobStores.jobStoreTest)
ensure_no_collisions() (in module toil.cwl.cwltoil)
enter() (toil.lib.threading.LastProcessStandingArena method)
envPrefix (toil.realtimeLogger.RealtimeLogger attribute)
ERROR (toil.batchSystems.abstractBatchSystem.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.lib.retry)
establish_boto3_session() (in module toil.lib.aws.session)
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)
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.version)
example_alwaysfail
module
example_cachingbenchmark
module
exc_info (toil.batchSystems.mesos.test.ExceptionalThread attribute)
(toil.lib.threading.ExceptionalThread attribute)
(toil.test.ExceptionalThread attribute)
ExceptionalThread (class in toil.batchSystems.mesos.test)
(class in toil.lib.threading)
(class in toil.test)
executor() (in module toil.batchSystems.contained_executor)
executorLost() (toil.batchSystems.mesos.batchSystem.MesosBatchSystem method)
exists() (toil.cwl.cwltoil.ToilFsAccess method)
(toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore.FileInfo class method)
(toil.server.wes.toil_backend.ToilWorkflow method)
exit_code (toil.bus.JobCompletedMessage attribute)
(toil.bus.JobStatus attribute)
EXIT_STATUS_UNAVAILABLE_VALUE (in module toil.batchSystems.abstractBatchSystem)
exitReason (toil.batchSystems.abstractBatchSystem.UpdatedBatchJobInfo attribute)
exitStatus (toil.batchSystems.abstractBatchSystem.UpdatedBatchJobInfo attribute)
Expando (class in toil.lib.expando)
expectedShutdownErrors() (in module toil.provisioners.aws.awsProvisioner)
explode() (in module example_alwaysfail)
export_file() (toil.common.Toil method)
(toil.fileStores.abstractFileStore.AbstractFileStore method)
(toil.fileStores.cachingFileStore.CachingFileStore method)
(toil.fileStores.nonCachingFileStore.NonCachingFileStore method)
(toil.jobStores.abstractJobStore.AbstractJobStore method)
exportFile() (toil.common.Toil method)
(toil.fileStores.abstractFileStore.AbstractFileStore method)
(toil.fileStores.cachingFileStore.CachingFileStore method)
(toil.fileStores.nonCachingFileStore.NonCachingFileStore method)
(toil.jobStores.abstractJobStore.AbstractJobStore method)
external_batch_id (toil.bus.ExternalBatchIdMessage attribute)
(toil.bus.JobStatus attribute)
ExternalBatchIdMessage (class in toil.bus)
externalStoreCache (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test attribute)
extract() (toil.cwl.cwltoil.CWLGather static method)
extractFile() (toil.provisioners.node.Node method)
F
f0() (in module toil.test.provisioners.restartScript)
FAILED (toil.batchSystems.abstractBatchSystem.BatchJobExitReason attribute)
FailedConstraint (in module toil.provisioners.clusterScaler)
FailedJobsException
failing_job_fn() (in module toil.test.src.busTest)
failingFn() (in module toil.test.src.restartDAGTest)
FailOnce (class in toil.test.src.checkpointTest)
fake_mpi_run
module
FakeBatchSystem (class in toil.test.batchSystems.test_slurm)
fallbackGetJobExitCode() (toil.batchSystems.lsf.LSFBatchSystem.Worker method)
fallbackRunningJobIDs() (toil.batchSystems.lsf.LSFBatchSystem.Worker method)
fC() (in module toil.common)
feed_deadlock_watchdog() (toil.leader.Leader method)
feed_flatcar_ami_release() (in module toil.lib.aws.ami)
fetch_and_unzip_from_s3() (toil.test.wdl.toilwdlTest.ToilWdlIntegrationTest class method)
fetch_call_outputs() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
fetch_ignoredifs() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
fetch_ignoredifs_chain() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
fetch_scatter_inputs() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
fetch_scatter_inputs_chain() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
fetch_scatter_outputs() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
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)
fetchEC2Index() (in module toil.lib.ec2nodes)
fetchEC2InstanceDict() (in module toil.lib.ec2nodes)
fetchFiles() (in module toil.test.utils.toilDebugTest)
fetchJobStoreFiles() (in module toil.utils.toilDebugFile)
fetchRootJob() (toil.utils.toilStatus.ToilStatus method)
fetchUserJobs() (toil.utils.toilStatus.ToilStatus method)
file_exists() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
fileContents (toil.test.jobStores.jobStoreTest.StubHttpRequestHandler attribute)
fileExists() (toil.jobStores.abstractJobStore.AbstractJobStore method)
FileID (class in toil.fileStores)
fileID (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo property)
fileIsCached() (toil.fileStores.cachingFileStore.CachingFileStore method)
FileJobStore (class in toil.jobStores.fileJobStore)
FileJobStoreTest (class in toil.test.jobStores.jobStoreTest)
FileResource (class in toil.resource)
files (toil.server.wes.amazon_wes_utils.WorkflowPlan attribute)
FilesDict (class in toil.server.wes.amazon_wes_utils)
fileSizeAndTime() (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.job.Promise attribute)
fileStore (toil.job.JobFunctionWrappingJob property)
(toil.job.ServiceHostJob 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)
filter_skip_null() (in module toil.cwl.cwltoil)
filtered_secondary_files() (in module toil.cwl.cwltoil)
filterServiceHosts() (toil.job.JobDescription method)
filterSuccessors() (toil.job.JobDescription method)
finalize_jobs() (in module debugWorkflow)
find() (in module toil.batchSystems.lsfHelper)
find_asts() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
find_default_container() (in module toil.cwl.cwltoil)
find_first_match() (in module toil.batchSystems.lsfHelper)
findMesosBinary() (toil.batchSystems.mesos.test.MesosTestSupport.MesosThread method)
FINISHED (toil.batchSystems.abstractBatchSystem.BatchJobExitReason attribute)
fits() (toil.provisioners.clusterScaler.NodeReservation method)
flat_crossproduct_scatter() (toil.cwl.cwltoil.CWLScatter method)
flatcar_release_feed_amis() (in module toil.lib.aws.ami)
FlatcarFeedTest (class in toil.test.lib.test_ec2)
flatten() (in module toil.lib.iterables)
(in module toil.wdl.wdl_functions)
flatten_tags() (in module toil.lib.aws.utils)
floor() (in module toil.wdl.wdl_functions)
flush() (toil.lib.io.WriteWatchingStream method)
fn() (in module tutorial_promises)
fn1Test() (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)
forgetJob() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.Worker method)
FORGO (in module toil.lib.docker)
format_std_out_err_glob() (toil.batchSystems.abstractBatchSystem.BatchSystemSupport method)
format_std_out_err_path() (toil.batchSystems.abstractBatchSystem.BatchSystemSupport method)
formatLogStream() (toil.statsAndLogging.StatsAndLogging class method)
forModule() (toil.resource.ModuleDescriptor class method)
forPath() (toil.fileStores.FileID class method)
frameworkMessage() (toil.batchSystems.mesos.batchSystem.MesosBatchSystem method)
(toil.batchSystems.mesos.executor.MesosExecutor method)
fromCommand() (toil.resource.ModuleDescriptor class method)
fromItem() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo class method)
full_policy() (toil.provisioners.aws.awsProvisioner.AWSProvisioner method)
FunctionWrappingJob (class in toil.job)
G
gatk_data (toil.test.wdl.toilwdlTest.ToilWdlIntegrationTest attribute)
gatk_data_dir (toil.test.wdl.toilwdlTest.ToilWdlIntegrationTest attribute)
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)
generate_attachment_path_names() (in module toil.server.cli.wes_cwl_runner)
generate_default_job_store() (in module toil.cwl.cwltoil)
generate_docker_bashscript_file() (in module toil.wdl.wdl_functions)
generate_locator() (in module toil.jobStores.utils)
generate_stdout_file() (in module toil.wdl.wdl_functions)
generateTorqueWrapper() (toil.batchSystems.torque.TorqueBatchSystem.Worker 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)
get_actions_from_policy_document() (in module toil.lib.aws.iam)
get_analyzer() (in module toil.wdl.utils)
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)
get_best_aws_zone() (in module toil.provisioners.aws)
get_bucket_region() (in module toil.lib.aws.utils)
get_conf_file() (in module toil.batchSystems.lsfHelper)
get_container_engine() (in module toil.cwl.cwltoil)
get_current_aws_region() (in module toil.lib.aws)
get_current_aws_zone() (in module toil.lib.aws)
get_current_state() (toil.server.utils.WorkflowStateMachine method)
get_default_kubernetes_owner() (toil.batchSystems.kubernetes.KubernetesBatchSystem class method)
get_default_mesos_endpoint() (toil.batchSystems.mesos.batchSystem.MesosBatchSystem class method)
get_default_tes_endpoint() (toil.batchSystems.tes.TESBatchSystem class method)
get_deps_from_cwltool() (in module toil.server.cli.wes_cwl_runner)
get_empty_file_store_id() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
get_env() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
get_error_body() (in module toil.lib.retry)
get_error_code() (in module toil.lib.retry)
get_error_message() (in module toil.lib.retry)
get_error_status() (in module toil.lib.retry)
get_failed_constraints() (toil.provisioners.clusterScaler.NodeReservation method)
get_file_class() (in module toil.server.utils)
get_file_paths_in_bindings() (in module toil.wdl.wdltoil)
get_file_size() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
get_flatcar_ami() (in module toil.lib.aws.ami)
get_free_snapshot() (toil.batchSystems.abstractBatchSystem.ResourceSet method)
get_health() (toil.server.wes.toil_backend.ToilBackend method)
get_homepage() (toil.server.wes.toil_backend.ToilBackend method)
get_host_accelerator_numbers() (in module toil.lib.accelerators)
get_individual_local_accelerators() (in module toil.lib.accelerators)
get_is_directory() (toil.jobStores.abstractJobStore.AbstractJobStore class method)
get_iso_time() (in module toil.server.utils)
get_job() (toil.toilState.ToilState method)
get_job_count() (toil.serviceManager.ServiceManager method)
get_job_kind() (toil.job.JobDescription method)
get_local_workflow_coordination_dir() (toil.common.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_object_for_url() (in module toil.lib.aws.utils)
get_omp_threads() (in module toil.test.batchSystems.batchSystemTest)
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)
get_process_name() (in module toil.lib.threading)
get_public_ip() (in module toil.lib.misc)
get_public_url() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
get_ready_client() (toil.serviceManager.ServiceManager method)
get_restrictive_environment_for_local_accelerators() (in module toil.lib.accelerators)
get_root_job_return_value() (toil.jobStores.abstractJobStore.AbstractJobStore method)
get_run_log() (toil.server.wes.abstract_backend.WESBackend method)
(toil.server.wes.toil_backend.ToilBackend method)
get_run_status() (toil.server.wes.abstract_backend.WESBackend method)
(toil.server.wes.toil_backend.ToilBackend method)
get_runs() (toil.server.wes.toil_backend.ToilBackend method)
get_service_info() (toil.server.wes.abstract_backend.WESBackend method)
(toil.server.wes.toil_backend.ToilBackend method)
get_shared_public_url() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
get_size() (toil.jobStores.abstractJobStore.AbstractJobStore class method)
(toil.jobStores.abstractJobStore.JobStoreSupport class method)
(toil.jobStores.aws.jobStore.AWSJobStore class method)
(toil.jobStores.fileJobStore.FileJobStore class method)
(toil.jobStores.googleJobStore.GoogleJobStore class method)
get_startable_service() (toil.serviceManager.ServiceManager method)
get_state() (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_stderr() (toil.server.wes.toil_backend.ToilBackend method)
get_stderr_path() (toil.server.wes.toil_backend.ToilWorkflow method)
get_stdout() (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.test)
get_toil_coordination_dir() (toil.common.Toil class method)
get_total_cpu_time() (in module toil.lib.resources)
get_total_cpu_time_and_memory_usage() (in module toil.lib.resources)
get_unservable_client() (toil.serviceManager.ServiceManager method)
get_user_name() (in module toil.lib.misc)
get_version() (in module toil.wdl.utils)
(toil.server.cli.wes_cwl_runner.WESClientWithWorkflowEngineParameters method)
getAdjacencyList() (toil.test.src.jobTest.JobTest static method)
getAutoscaledInstanceShapes() (toil.provisioners.abstractProvisioner.AbstractProvisioner method)
getAverageRuntime() (toil.provisioners.clusterScaler.ClusterScaler method)
getBaseInstanceConfiguration() (toil.provisioners.abstractProvisioner.AbstractProvisioner method)
getBatchSystemID() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.Worker 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.job.Job.Runner static method)
getDefaultOptions() (toil.job.Job.Runner static method)
getDirSizeRecursively() (in module toil.common)
getEmptyFileStoreID() (toil.jobStores.abstractJobStore.AbstractJobStore method)
getEnv() (toil.jobStores.abstractJobStore.AbstractJobStore method)
getEnvString() (toil.batchSystems.htcondor.HTCondorBatchSystem.Worker method)
getEstimatedNodeCounts() (toil.provisioners.clusterScaler.ClusterScaler method)
getFileReaderCount() (toil.fileStores.cachingFileStore.CachingFileStore method)
getFileSize() (toil.jobStores.abstractJobStore.AbstractJobStore method)
getFileSystemSize() (in module toil.common)
getGlobalFileSize() (toil.fileStores.abstractFileStore.AbstractFileStore method)
getIssuedBatchJobIDs() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
(toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem method)
(toil.batchSystems.awsBatch.AWSBatchBatchSystem method)
(toil.batchSystems.kubernetes.KubernetesBatchSystem method)
(toil.batchSystems.mesos.batchSystem.MesosBatchSystem method)
(toil.batchSystems.parasol.ParasolBatchSystem method)
(toil.batchSystems.singleMachine.SingleMachineBatchSystem method)
(toil.batchSystems.tes.TESBatchSystem method)
getIssuedLocalJobIDs() (toil.batchSystems.local_support.BatchSystemLocalSupport method)
getJobExitCode() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.Worker method)
(toil.batchSystems.gridengine.GridEngineBatchSystem.Worker method)
(toil.batchSystems.htcondor.HTCondorBatchSystem.Worker method)
(toil.batchSystems.lsf.LSFBatchSystem.Worker method)
(toil.batchSystems.slurm.SlurmBatchSystem.Worker method)
(toil.batchSystems.torque.TorqueBatchSystem.Worker method)
getJobExitCodeBACCT() (toil.batchSystems.lsf.LSFBatchSystem.Worker method)
getJobIDsForResultsFile() (toil.batchSystems.parasol.ParasolBatchSystem method)
getJobs() (toil.leader.Leader method)
(toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method)
getJobStore() (toil.common.Toil class method)
getKubernetesAutoscalerSetupCommands() (toil.provisioners.abstractProvisioner.AbstractProvisioner method)
(toil.provisioners.aws.awsProvisioner.AWSProvisioner method)
getKubernetesCloudProvider() (toil.provisioners.abstractProvisioner.AbstractProvisioner method)
(toil.provisioners.aws.awsProvisioner.AWSProvisioner method)
getKubernetesValues() (toil.provisioners.abstractProvisioner.AbstractProvisioner method)
getLeader() (toil.provisioners.abstractProvisioner.AbstractProvisioner method)
(toil.provisioners.aws.awsProvisioner.AWSProvisioner method)
(toil.provisioners.gceProvisioner.GCEProvisioner method)
(toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method)
getLocalTempDir() (toil.fileStores.abstractFileStore.AbstractFileStore method)
getLocalTempFile() (toil.fileStores.abstractFileStore.AbstractFileStore method)
getLocalTempFileName() (toil.fileStores.abstractFileStore.AbstractFileStore method)
getLocalWorkflowDir() (toil.common.Toil class method)
getLogFileHandle() (toil.job.JobDescription method)
getLogger() (toil.realtimeLogger.RealtimeLogger class method)
getLogLevelString() (in module toil.lib.bioio)
getMidPoint() (in module toil.test.sort.restart_sort)
(in module toil.test.sort.sort)
getNextJobID() (toil.batchSystems.local_support.BatchSystemLocalSupport method)
getNodeID() (in module toil.common)
getNodes() (toil.batchSystems.abstractBatchSystem.AbstractScalableBatchSystem method)
(toil.batchSystems.mesos.batchSystem.MesosBatchSystem method)
(toil.provisioners.clusterScaler.ClusterScaler method)
(toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method)
getNodeShape() (toil.provisioners.abstractProvisioner.AbstractProvisioner method)
(toil.provisioners.aws.awsProvisioner.AWSProvisioner method)
(toil.provisioners.gceProvisioner.GCEProvisioner 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.utils.toilStatus.ToilStatus static method)
getProvisionedWorkers() (toil.provisioners.abstractProvisioner.AbstractProvisioner method)
(toil.provisioners.aws.awsProvisioner.AWSProvisioner method)
(toil.provisioners.gceProvisioner.GCEProvisioner method)
(toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method)
getPublicUrl() (toil.jobStores.abstractJobStore.AbstractJobStore method)
getRandomEdge() (toil.test.src.jobTest.JobTest static method)
getRequiredNodes() (toil.provisioners.clusterScaler.BinPackedFit method)
getRootJobReturnValue() (toil.jobStores.abstractJobStore.AbstractJobStore method)
getRootJobs() (toil.job.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.kubernetes.KubernetesBatchSystem method)
(toil.batchSystems.mesos.batchSystem.MesosBatchSystem method)
(toil.batchSystems.parasol.ParasolBatchSystem method)
(toil.batchSystems.singleMachine.SingleMachineBatchSystem method)
(toil.batchSystems.tes.TESBatchSystem method)
getRunningJobIDs() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.Worker method)
(toil.batchSystems.gridengine.GridEngineBatchSystem.Worker method)
(toil.batchSystems.htcondor.HTCondorBatchSystem.Worker method)
(toil.batchSystems.lsf.LSFBatchSystem.Worker method)
(toil.batchSystems.slurm.SlurmBatchSystem.Worker method)
(toil.batchSystems.torque.TorqueBatchSystem.Worker method)
getRunningLocalJobIDs() (toil.batchSystems.local_support.BatchSystemLocalSupport method)
getSchedulingStatusMessage() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
(toil.batchSystems.singleMachine.SingleMachineBatchSystem method)
getSharedPublicUrl() (toil.jobStores.abstractJobStore.AbstractJobStore method)
getSize() (toil.jobStores.abstractJobStore.AbstractJobStore class method)
(toil.jobStores.aws.jobStore.AWSJobStore.FileInfo method)
getSpaceUsableForJobs() (toil.fileStores.cachingFileStore.CachingFileStore method)
getStaticNodes() (toil.provisioners.clusterScaler.ClusterScaler method)
getStats() (in module toil.utils.toilStats)
getStatus() (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.common.Toil static method)
getTopologicalOrderingOfJobs() (toil.job.Job method)
getUpdatedBatchJob() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
(toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem method)
(toil.batchSystems.awsBatch.AWSBatchBatchSystem method)
(toil.batchSystems.kubernetes.KubernetesBatchSystem method)
(toil.batchSystems.mesos.batchSystem.MesosBatchSystem method)
(toil.batchSystems.parasol.ParasolBatchSystem method)
(toil.batchSystems.singleMachine.SingleMachineBatchSystem method)
(toil.batchSystems.tes.TESBatchSystem method)
(toil.batchSystems.torque.TorqueBatchSystem.Worker method)
getUpdatedLocalJob() (toil.batchSystems.local_support.BatchSystemLocalSupport method)
getUserScript() (toil.job.EncapsulatedJob method)
(toil.job.FunctionWrappingJob method)
(toil.job.Job method)
(toil.job.ServiceHostJob method)
getValue() (toil.job.PromisedRequirement method)
getWaitDuration() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem class method)
(toil.batchSystems.gridengine.GridEngineBatchSystem class method)
(toil.batchSystems.lsf.LSFBatchSystem method)
(toil.batchSystems.mesos.batchSystem.MesosBatchSystem method)
(toil.test.batchSystems.test_slurm.FakeBatchSystem method)
getWidth() (toil.utils.toilStats.ColumnWidths method)
getWorkerContexts() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
(toil.batchSystems.cleanup_support.BatchSystemCleanupSupport method)
getWorkersInCluster() (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method)
glob() (in module toil.lib.resources)
(toil.cwl.cwltoil.ToilFsAccess method)
global_mutex() (in module toil.lib.threading)
globalFileStoreJobFn() (in module tutorial_managing2)
globalize() (toil.resource.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)
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)
greatGrandChild() (in module toil.test.batchSystems.batchSystemTest)
gridengine_batch_system_factory() (in module toil.batchSystems.registry)
GridEngineBatchSystem (class in toil.batchSystems.gridengine)
GridEngineBatchSystem.Worker (class in toil.batchSystems.gridengine)
GridEngineBatchSystemTest (class in toil.test.batchSystems.batchSystemTest)
GunicornApplication (class in toil.server.wsgi_app)
H
handle() (toil.realtimeLogger.LoggingDatagramHandler method)
handle_errors() (in module toil.server.wes.abstract_backend)
handleLocalJob() (toil.batchSystems.local_support.BatchSystemLocalSupport method)
hasAutoscaledNodeTypes() (toil.provisioners.abstractProvisioner.AbstractProvisioner method)
hasChild() (toil.cwl.cwltoil.SelfJob method)
(toil.job.Job method)
(toil.job.JobDescription method)
hasFollowOn() (toil.job.Job method)
(toil.job.JobDescription method)
hasPredecessor() (toil.job.Job method)
hasService() (toil.job.Job method)
hasServiceHostJob() (toil.job.JobDescription method)
HAVE_S3 (in module toil.server.utils)
have_working_nvidia_docker_runtime() (in module toil.lib.accelerators)
(in module toil.test)
have_working_nvidia_smi() (in module toil.lib.accelerators)
(in module toil.test)
headers (toil.test.jobStores.jobStoreTest.GoogleJobStoreTest attribute)
hello_world() (in module toil.test.mesos.helloWorld)
hello_world_child() (in module toil.test.mesos.helloWorld)
HelloWorld (class in toil.test.src.helloWorldTest)
(class in toil.test.src.toilContextManagerTest)
(class in tutorial_arguments)
(class in tutorial_invokeworkflow)
(class in tutorial_invokeworkflow2)
(class in tutorial_staging)
helloWorld() (in module tutorial_helloworld)
(in module tutorial_jobfunctions)
(in module tutorial_multiplejobs)
(in module tutorial_multiplejobs2)
(in module tutorial_multiplejobs3)
(in module tutorial_quickstart)
HelloWorldFollowOn (class in toil.test.mesos.stress)
HelloWorldJob (class in toil.test.mesos.stress)
HelloWorldTest (class in toil.test.src.helloWorldTest)
heredoc_wdl() (in module toil.wdl.wdl_functions)
hidden (class in toil.test.batchSystems.batchSystemTest)
(class in toil.test.server.serverTest)
(class in toil.test.src.fileStoreTest)
(class in toil.test.src.promisedRequirementTest)
hidden.AbstractBatchSystemJobTest (class in toil.test.batchSystems.batchSystemTest)
hidden.AbstractBatchSystemTest (class in toil.test.batchSystems.batchSystemTest)
hidden.AbstractCachingFileStoreTest (class in toil.test.src.fileStoreTest)
hidden.AbstractFileStoreTest (class in toil.test.src.fileStoreTest)
hidden.AbstractGridEngineBatchSystemTest (class in toil.test.batchSystems.batchSystemTest)
hidden.AbstractNonCachingFileStoreTest (class in toil.test.src.fileStoreTest)
hidden.AbstractPromisedRequirementsTest (class in toil.test.src.promisedRequirementTest)
hidden.AbstractStateStoreTest (class in toil.test.server.serverTest)
hms_duration_to_seconds() (in module toil.lib.conversions)
htcondor_batch_system_factory() (in module toil.batchSystems.registry)
HTCondorBatchSystem (class in toil.batchSystems.htcondor)
HTCondorBatchSystem.Worker (class in toil.batchSystems.htcondor)
HTCondorBatchSystemTest (class in toil.test.batchSystems.batchSystemTest)
human2bytes() (in module toil.lib.conversions)
(in module toil.lib.humanize)
I
iam_client (in module toil.lib.ec2)
IAMTest (class in toil.test.lib.aws.test_iam)
iC() (in module toil.common)
ignoreNode() (toil.batchSystems.abstractBatchSystem.AbstractScalableBatchSystem method)
(toil.batchSystems.mesos.batchSystem.MesosBatchSystem method)
(toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method)
IllegalDeletionCacheError
import_file() (toil.common.Toil method)
(toil.fileStores.abstractFileStore.AbstractFileStore method)
(toil.jobStores.abstractJobStore.AbstractJobStore method)
import_files() (in module toil.cwl.cwltoil)
(in module toil.wdl.wdltoil)
ImportExportFileTest (class in toil.test.src.importExportFileTest)
importFile() (toil.common.Toil method)
(toil.fileStores.abstractFileStore.AbstractFileStore method)
(toil.jobStores.abstractJobStore.AbstractJobStore method)
in_contexts() (in module toil.worker)
inconsistencies_detected() (in module toil.lib.ec2)
INCONSISTENCY_ERRORS (in module toil.lib.ec2)
indent() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
Info (class in toil.batchSystems.singleMachine)
init() (toil.server.wsgi_app.GunicornApplication method)
init_action_collection() (in module toil.lib.aws.iam)
initialize() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
initialize_jobs() (in module debugWorkflow)
(in module tutorial_cwlexample)
initialize_run() (toil.server.wes.tasks.ToilWorkflowRunner method)
initialized (toil.realtimeLogger.RealtimeLogger attribute)
injectFile() (toil.provisioners.node.Node method)
InnerClass (class in toil.lib.objects)
innerLoop() (toil.leader.Leader method)
insertJob() (toil.batchSystems.mesos.JobQueue method)
instance_type (toil.bus.ClusterDesiredSizeMessage attribute)
(toil.bus.ClusterSizeMessage attribute)
InstanceType (class in toil.lib.ec2nodes)
InsufficientSystemResources
integrative() (in module toil.test)
internet_connection() (in module toil.utils.toilUpdateEC2Instances)
InvalidAWSJobStoreTest (class in toil.test.jobStores.jobStoreTest)
InvalidClusterStateException
InvalidImportExportUrlException
InvalidSourceCacheError
InvalidVersion
inVirtualEnv() (in module toil)
invoke() (toil.deferred.DeferredFunction method)
is_active() (toil.serviceManager.ServiceManager method)
is_context() (in module toil.wdl.versions.v1)
is_false() (toil.cwl.cwltoil.Conditional method)
is_number() (in module toil.wdl.wdl_functions)
is_ok() (toil.server.wes.tasks.MultiprocessingTaskRunner class method)
(toil.server.wes.tasks.TaskRunner static method)
is_retryable_kubernetes_error() (in module toil.batchSystems.kubernetes)
is_running() (toil.serviceManager.ServiceManager method)
is_subtree_done() (toil.job.JobDescription method)
isAcyclic() (toil.test.src.jobTest.JobTest method)
isdir() (toil.cwl.cwltoil.ToilFsAccess method)
isfile() (toil.cwl.cwltoil.ToilFsAccess method)
isNumber() (in module toil.lib.ec2nodes)
issueBatchJob() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
(toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem method)
(toil.batchSystems.awsBatch.AWSBatchBatchSystem method)
(toil.batchSystems.htcondor.HTCondorBatchSystem method)
(toil.batchSystems.kubernetes.KubernetesBatchSystem method)
(toil.batchSystems.mesos.batchSystem.MesosBatchSystem method)
(toil.batchSystems.parasol.ParasolBatchSystem method)
(toil.batchSystems.singleMachine.SingleMachineBatchSystem method)
(toil.batchSystems.tes.TESBatchSystem 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)
ItemT (toil.batchSystems.kubernetes.KubernetesBatchSystem attribute)
J
j (in module tutorial_services)
Job (class in toil.job)
Job.Runner (class in toil.job)
Job.Service (class in toil.job)
JOB_DIR_PREFIX (toil.jobStores.fileJobStore.FileJobStore attribute)
job_exists() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
(toil.toilState.ToilState 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)
JOB_NAME_DIR_PREFIX (toil.jobStores.fileJobStore.FileJobStore attribute)
job_store_id (toil.bus.JobStatus attribute)
job_type (toil.bus.JobCompletedMessage attribute)
(toil.bus.JobFailedMessage attribute)
(toil.bus.JobIssuedMessage attribute)
JobAnnotationMessage (class in toil.bus)
JobClass (class in toil.test.src.userDefinedJobArgTypeTest)
JobCompletedMessage (class in toil.bus)
JobDescription (class in toil.job)
JobDescriptionTest (class in toil.test.src.jobDescriptionTest)
JobEncapsulationTest (class in toil.test.src.jobEncapsulationTest)
JobException
JobFailedMessage (class in toil.bus)
JobFileStoreTest (class in toil.test.src.jobFileStoreTest)
jobFunction() (in module toil.test.src.userDefinedJobArgTypeTest)
JobFunctionWrappingJob (class in toil.job)
JobGraphDeadlockException
jobID (toil.batchSystems.abstractBatchSystem.UpdatedBatchJobInfo attribute)
jobIDs() (toil.batchSystems.mesos.JobQueue method)
JobIssuedMessage (class in toil.bus)
JobMissingMessage (class in toil.bus)
JobPromiseConstraintError
JobQueue (class in toil.batchSystems.mesos)
jobs (toil.worker.StatsDict attribute)
jobs() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
JobServiceTest (class in toil.test.src.jobServiceTest)
jobsPerBatchInsert (toil.jobStores.aws.jobStore.AWSJobStore attribute)
JobStatus (class in toil.bus)
jobstore (in module tutorial_cwlexample)
(in module tutorial_docker)
(in module tutorial_dynamic)
(in module tutorial_invokeworkflow)
(in module tutorial_invokeworkflow2)
(in module tutorial_jobfunctions)
(in module tutorial_managing)
(in module tutorial_managing2)
(in module tutorial_promises)
(in module tutorial_promises2)
(in module tutorial_quickstart)
(in module tutorial_requirements)
(in module tutorial_services)
(in module tutorial_staging)
jobStore (toil.common.Config attribute)
JOBSTORE_HELP (in module toil.common)
JobStoreExistsException
jobStoreID (toil.job.Job property)
jobStorePath (in module debugWorkflow)
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
JobTest (class in toil.test.src.jobTest)
JobTooBigError
JobTuple (in module toil.batchSystems.abstractGridEngineBatchSystem)
(in module toil.batchSystems.htcondor)
JobUpdatedMessage (class in toil.bus)
join() (toil.batchSystems.mesos.test.ExceptionalThread method)
(toil.cwl.cwltoil.ToilFsAccess method)
(toil.lib.threading.ExceptionalThread method)
(toil.test.ExceptionalThread method)
json_var() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
JSONDatagramHandler (class in toil.realtimeLogger)
JustAValue (class in toil.cwl.cwltoil)
K
keys() (in module toil.wdl.wdl_functions)
KeyValuesList (in module toil.batchSystems.kubernetes)
kill_services() (toil.serviceManager.ServiceManager method)
killBatchJobs() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
(toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem method)
(toil.batchSystems.awsBatch.AWSBatchBatchSystem method)
(toil.batchSystems.kubernetes.KubernetesBatchSystem method)
(toil.batchSystems.mesos.batchSystem.MesosBatchSystem method)
(toil.batchSystems.parasol.ParasolBatchSystem method)
(toil.batchSystems.singleMachine.SingleMachineBatchSystem method)
(toil.batchSystems.tes.TESBatchSystem method)
KILLED (toil.batchSystems.abstractBatchSystem.BatchJobExitReason attribute)
killJob() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.Worker method)
(toil.batchSystems.gridengine.GridEngineBatchSystem.Worker method)
(toil.batchSystems.htcondor.HTCondorBatchSystem.Worker method)
(toil.batchSystems.lsf.LSFBatchSystem.Worker method)
(toil.batchSystems.slurm.SlurmBatchSystem.Worker method)
(toil.batchSystems.torque.TorqueBatchSystem.Worker method)
killJobs() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.Worker method)
(toil.leader.Leader method)
killLocalJobs() (toil.batchSystems.local_support.BatchSystemLocalSupport method)
killTask() (toil.batchSystems.mesos.executor.MesosExecutor method)
kind (toil.job.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.kubernetes.KubernetesBatchSystem.KubernetesConfig attribute)
kubernetes_owner (toil.batchSystems.kubernetes.KubernetesBatchSystem.KubernetesConfig attribute)
kubernetes_pod_timeout (toil.batchSystems.kubernetes.KubernetesBatchSystem.KubernetesConfig attribute)
kubernetes_policy() (toil.provisioners.aws.awsProvisioner.AWSProvisioner method)
kubernetes_service_account (toil.batchSystems.kubernetes.KubernetesBatchSystem.KubernetesConfig 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.lib.threading)
launchCluster() (toil.provisioners.abstractProvisioner.AbstractProvisioner method)
(toil.provisioners.aws.awsProvisioner.AWSProvisioner method)
(toil.provisioners.gceProvisioner.GCEProvisioner method)
(toil.test.provisioners.aws.awsProvisionerTest.AWSAutoscaleTest method)
(toil.test.provisioners.aws.awsProvisionerTest.AWSManagedAutoscaleTest method)
(toil.test.provisioners.aws.awsProvisionerTest.AWSStaticAutoscaleTest 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)
launchTask() (toil.batchSystems.mesos.executor.MesosExecutor method)
Leader (class in toil.leader)
LEADER_HOME_DIR (toil.provisioners.abstractProvisioner.AbstractProvisioner attribute)
leave() (toil.lib.threading.LastProcessStandingArena method)
length() (in module toil.wdl.wdl_functions)
link_file() (in module toil.server.utils)
link_merge() (toil.cwl.cwltoil.ResolveSource method)
list_objects_for_url() (in module toil.lib.aws.utils)
list_runs() (toil.server.wes.abstract_backend.WESBackend method)
(toil.server.wes.toil_backend.ToilBackend method)
list_url() (toil.jobStores.abstractJobStore.AbstractJobStore class method)
listdir() (toil.cwl.cwltoil.ToilFsAccess method)
load() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore.FileInfo class method)
(toil.resource.ModuleDescriptor method)
(toil.server.wsgi_app.GunicornApplication method)
load_config() (toil.server.wsgi_app.GunicornApplication method)
load_contents() (toil.test.cwl.cwlTest.CWLWorkflowTest method)
load_job() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
load_root_job() (toil.jobStores.abstractJobStore.AbstractJobStore method)
load_workflow() (toil.toilState.ToilState method)
loadJob() (toil.job.Job class method)
loadModules() (in module toil.utils.toilMain)
loadOrCreate() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo class method)
loadOrFail() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo class method)
loadRootJob() (toil.jobStores.abstractJobStore.AbstractJobStore method)
localDirPath (toil.resource.Resource property)
LocalFileStoreJob (class in tutorial_managing)
localize() (toil.resource.ModuleDescriptor method)
localPath (toil.resource.DirectoryResource property)
(toil.resource.FileResource property)
(toil.resource.Resource property)
LocalThrottle (class in toil.lib.throttle)
locator (toil.jobStores.abstractJobStore.AbstractJobStore property)
lock (toil.batchSystems.mesos.test.MesosTestSupport.MesosThread attribute)
(toil.realtimeLogger.RealtimeLogger attribute)
(toil.test.ApplianceTestSupport.Appliance attribute)
(toil.test.batchSystems.parasolTestSupport.ParasolTestSupport.ParasolThread 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.batchSystems.parasolTestSupport)
(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.job.Job method)
log_bindings() (in module toil.wdl.wdltoil)
log_for_run() (toil.server.wes.abstract_backend.WESBackend static method)
log_to_file() (in module toil.statsAndLogging)
logAccess() (toil.fileStores.abstractFileStore.AbstractFileStore method)
logClusterDesiredSize() (toil.common.ToilMetrics method)
logClusterSize() (toil.common.ToilMetrics method)
logCompletedJob() (toil.common.ToilMetrics method)
logDiskUsage() (in module toil.test.src.promisedRequirementTest)
logFailedJob() (toil.common.ToilMetrics method)
logFile (toil.common.Config attribute)
logger (in module debugWorkflow)
(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.parasol)
(in module toil.batchSystems.registry)
(in module toil.batchSystems.singleMachine)
(in module toil.batchSystems.slurm)
(in module toil.batchSystems.tes)
(in module toil.batchSystems.torque)
(in module toil.bus)
(in module toil.common)
(in module toil.cwl)
(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.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.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.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.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.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.toilwdl)
(in module toil.wdl.versions.dev)
(in module toil.wdl.versions.draft2)
(in module toil.wdl.versions.v1)
(in module toil.wdl.wdl_analysis)
(in module toil.wdl.wdl_functions)
(in module toil.wdl.wdl_synthesis)
(in module toil.wdl.wdltoil)
(in module toil.worker)
(toil.realtimeLogger.RealtimeLogger attribute)
LoggingDatagramHandler (class in toil.realtimeLogger)
loggingServer (toil.realtimeLogger.RealtimeLogger attribute)
loginCredentialsPromise (in module tutorial_services)
logIssuedJob() (toil.common.ToilMetrics method)
logMissingJob() (toil.common.ToilMetrics method)
logProcessContext() (in module toil)
logQueueSize() (toil.common.ToilMetrics method)
logRotating (toil.common.Config attribute)
LogTest (class in toil.test.src.realtimeLoggerTest)
logToMaster() (toil.fileStores.abstractFileStore.AbstractFileStore method)
logWithFormatting() (toil.statsAndLogging.StatsAndLogging class method)
LongTestFollowOn (class in toil.test.mesos.stress)
LongTestJob (class in toil.test.mesos.stress)
lookup() (toil.resource.Resource class method)
lookupEnvVar() (in module toil)
LOST (toil.batchSystems.abstractBatchSystem.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.Worker (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)
main() (in module example_alwaysfail)
(in module example_cachingbenchmark)
(in module mkFile)
(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.src.userDefinedJobArgTypeTest)
(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.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.toilwdl)
(in module toil.wdl.wdltoil)
(in module toil.worker)
(in module tutorial_discoverfiles)
mainCacheTag (in module toil.version)
make_gather_bindings() (toil.wdl.wdltoil.WDLSectionJob method)
make_parser() (in module fake_mpi_run)
make_path_mapper() (toil.cwl.cwltoil.ToilTool method)
make_public_dir() (in module toil.lib.io)
make_tests() (in module toil.test)
makeFileToSort() (in module toil.test.sort.restart_sort)
(in module toil.test.sort.sort)
makeImportExportTests() (toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test class method)
makeJob() (in module toil.cwl.cwltoil)
makeJobGraph() (toil.test.src.jobTest.JobTest method)
makeLoadable() (toil.resource.ModuleDescriptor method)
makePickle() (toil.realtimeLogger.JSONDatagramHandler method)
makeRandomDAG() (toil.test.src.jobTest.JobTest static method)
MalformedRequestException
ManagedNodesNotSupportedException
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.common.Config attribute)
max_local_jobs (toil.common.Config attribute)
MAX_POLL_COUNT (in module toil.batchSystems.awsBatch)
maxAttributesPerItem (toil.jobStores.aws.utils.SDBHelper attribute)
maxBinarySize() (toil.jobStores.aws.utils.SDBHelper class method)
maxBucketNameLen (toil.jobStores.aws.jobStore.AWSJobStore attribute)
maxConcurrency() (in module toil.test.src.promisedRequirementTest)
MaxCoresSingleMachineBatchSystemTest (class in toil.test.batchSystems.batchSystemTest)
maxInlinedSize() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo static method)
maxNameLen (toil.jobStores.aws.jobStore.AWSJobStore attribute)
maxRawValueSize (toil.jobStores.aws.utils.SDBHelper attribute)
maxValueSize (toil.jobStores.aws.utils.SDBHelper attribute)
maxWaitTime (toil.provisioners.node.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)
memoize (in module toil)
(in module toil.lib.memoize)
(in module toil.test)
memory (toil.job.Job property)
(toil.job.RequirementsDict attribute)
(toil.job.Requirer 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 tutorial_promises2)
mesos_batch_system_factory() (in module toil.batchSystems.registry)
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)
MesosExecutor (class in toil.batchSystems.mesos.executor)
MesosPromisedRequirementsTest (class in toil.test.src.promisedRequirementTest)
MesosShape (class in toil.batchSystems.mesos)
MesosTestSupport (class in toil.batchSystems.mesos.test)
MesosTestSupport.MesosAgentThread (class in toil.batchSystems.mesos.test)
MesosTestSupport.MesosMasterThread (class in toil.batchSystems.mesos.test)
MesosTestSupport.MesosThread (class in toil.batchSystems.mesos.test)
message (toil.fileStores.cachingFileStore.CacheUnbalancedError attribute)
message_to_bytes() (in module toil.bus)
MessageBus (class in toil.bus)
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.bus)
MessageType (in module toil.bus)
(toil.bus.MessageBus attribute)
(toil.bus.MessageInbox attribute)
methodNamePartRegex (in module toil.test)
mib_to_b() (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)
minCores (toil.batchSystems.singleMachine.SingleMachineBatchSystem attribute)
MiscTests (class in toil.test.src.miscTests)
mkFile
module
MockBatchSystemAndProvisioner (class in toil.test.provisioners.clusterScalerTest)
model (toil.job.AcceleratorRequirement attribute)
modify_cmd_expr_w_attributes() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
modify_param_paths() (toil.server.cli.wes_cwl_runner.WESClientWithWorkflowEngineParameters method)
module
debugWorkflow
example_alwaysfail
example_cachingbenchmark
fake_mpi_run
mkFile
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.parasol
toil.batchSystems.registry
toil.batchSystems.singleMachine
toil.batchSystems.slurm
toil.batchSystems.tes
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._dummy
toil.lib.encryption._nacl
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.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.batchSystemTest
toil.test.batchSystems.parasolTestSupport
toil.test.batchSystems.test_lsf_helper
toil.test.batchSystems.test_slurm
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.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.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.builtinTest
toil.test.wdl.conftest
toil.test.wdl.toilwdlTest
toil.test.wdl.wdltoil_test
toil.toilState
toil.utils
toil.utils.toilClean
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.toilwdl
toil.wdl.utils
toil.wdl.versions
toil.wdl.versions.dev
toil.wdl.versions.draft2
toil.wdl.versions.v1
toil.wdl.wdl_analysis
toil.wdl.wdl_functions
toil.wdl.wdl_synthesis
toil.wdl.wdl_types
toil.wdl.wdltoil
toil.worker
tutorial_arguments
tutorial_cwlexample
tutorial_discoverfiles
tutorial_docker
tutorial_dynamic
tutorial_encapsulation
tutorial_encapsulation2
tutorial_helloworld
tutorial_invokeworkflow
tutorial_invokeworkflow2
tutorial_jobfunctions
tutorial_managing
tutorial_managing2
tutorial_multiplejobs
tutorial_multiplejobs2
tutorial_multiplejobs3
tutorial_promises
tutorial_promises2
tutorial_quickstart
tutorial_requirements
tutorial_services
tutorial_staging
ModuleDescriptor (class in toil.resource)
monkeyPatchSdbConnection() (in module toil.jobStores.aws.utils)
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)
N
name (toil.bus.JobStatus attribute)
(toil.resource.ModuleDescriptor attribute)
(toil.wdl.wdl_types.WDLArrayType property)
(toil.wdl.wdl_types.WDLBooleanType property)
(toil.wdl.wdl_types.WDLFileType property)
(toil.wdl.wdl_types.WDLFloatType property)
(toil.wdl.wdl_types.WDLIntType property)
(toil.wdl.wdl_types.WDLMapType property)
(toil.wdl.wdl_types.WDLPairType property)
(toil.wdl.wdl_types.WDLStringType property)
(toil.wdl.wdl_types.WDLType property)
nameSeparator (toil.jobStores.aws.jobStore.AWSJobStore attribute)
needs_aws_batch() (in module toil.test)
needs_aws_ec2() (in module toil.test)
needs_aws_s3() (in module toil.test)
needs_celery_broker() (in module toil.test)
needs_cwl() (in module toil.test)
needs_docker() (in module toil.test)
needs_docker_cuda() (in module toil.test)
needs_encryption() (in module toil.test)
needs_env_var() (in module toil.test)
needs_fetchable_appliance() (in module toil.test)
needs_file_import() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
needs_google_project() (in module toil.test)
needs_google_storage() (in module toil.test)
needs_gridengine() (in module toil.test)
needs_htcondor() (in module toil.test)
needs_java() (in module toil.test)
needs_kubernetes() (in module toil.test)
needs_kubernetes_installed() (in module toil.test)
needs_local_appliance() (in module toil.test)
needs_local_cuda() (in module toil.test)
needs_lsf() (in module toil.test)
needs_mesos() (in module toil.test)
needs_parasol() (in module toil.test)
needs_rsync3() (in module toil.test)
needs_server() (in module toil.test)
needs_singularity() (in module toil.test)
needs_singularity_or_docker() (in module toil.test)
needs_slurm() (in module toil.test)
needs_tes() (in module toil.test)
needs_torque() (in module toil.test)
needs_wes_server() (in module toil.test)
needsdocker() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
nested_crossproduct_scatter() (toil.cwl.cwltoil.CWLScatter method)
nextChainable() (in module toil.worker)
nextJobOfType() (toil.batchSystems.mesos.JobQueue method)
nextSuccessors() (toil.job.JobDescription method)
no_such_sdb_domain() (in module toil.jobStores.aws.utils)
NoAvailableJobStoreException
Node (class in toil.provisioners.node)
NODE_BOTO_PATH (toil.provisioners.gceProvisioner.GCEProvisioner attribute)
NodeInfo (class in toil.batchSystems.abstractBatchSystem)
nodeInUse() (toil.batchSystems.abstractBatchSystem.AbstractScalableBatchSystem method)
(toil.batchSystems.mesos.batchSystem.MesosBatchSystem method)
(toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method)
NodeReservation (class in toil.provisioners.clusterScaler)
nodeReservations (toil.provisioners.clusterScaler.BinPackedFit attribute)
nodeServiceAccountJson (toil.jobStores.googleJobStore.GoogleJobStore 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)
noOp() (in module toil.test.src.jobEncapsulationTest)
normalize_uri() (toil.common.Toil static method)
NoSuchClusterException
NoSuchFileException
NoSuchJobException
NoSuchJobStoreException
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.singleMachine.SingleMachineBatchSystem attribute)
O
old_retry() (in module toil.lib.retry)
onRegistration() (toil.job.JobDescription method)
(toil.job.ServiceJobDescription method)
onWrite() (toil.lib.io.WriteWatchingStream method)
open() (toil.cwl.cwltoil.ToilFsAccess method)
(toil.deferred.DeferredFunctionManager method)
(toil.fileStores.abstractFileStore.AbstractFileStore method)
(toil.fileStores.cachingFileStore.CachingFileStore method)
(toil.fileStores.nonCachingFileStore.NonCachingFileStore method)
OperationForbidden
optimize_spot_bid() (in module toil.provisioners.aws)
optional_hard_copy() (toil.jobStores.fileJobStore.FileJobStore method)
OptionSetter (class in toil.batchSystems.options)
OptionType (toil.batchSystems.kubernetes.KubernetesBatchSystem attribute)
(toil.batchSystems.options.OptionSetter attribute)
(toil.batchSystems.slurm.SlurmBatchSystem attribute)
OS_SIZE (in module toil.provisioners.clusterScaler)
outbox() (toil.bus.MessageBus method)
outer (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo attribute)
overhead (in module toil.lib.encryption._dummy)
(in module toil.lib.encryption._nacl)
ownerID (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo property)
P
P (toil.batchSystems.kubernetes.KubernetesBatchSystem attribute)
(toil.batchSystems.kubernetes.KubernetesBatchSystem.DecoratorWrapper attribute)
pack() (toil.fileStores.FileID method)
pack_job() (in module toil.batchSystems.contained_executor)
pack_toil_uri() (in module toil.wdl.wdltoil)
padStr() (in module toil.utils.toilStats)
panic (class in toil.lib.exceptions)
parasol_batch_system_factory() (in module toil.batchSystems.registry)
ParasolBatchSystem (class in toil.batchSystems.parasol)
ParasolBatchSystemTest (class in toil.test.batchSystems.batchSystemTest)
parasolCommand() (toil.test.batchSystems.parasolTestSupport.ParasolTestSupport.ParasolLeaderThread method)
(toil.test.batchSystems.parasolTestSupport.ParasolTestSupport.ParasolThread method)
(toil.test.batchSystems.parasolTestSupport.ParasolTestSupport.ParasolWorkerThread method)
parasolOutputPattern (toil.batchSystems.parasol.ParasolBatchSystem attribute)
ParasolTestSupport (class in toil.test.batchSystems.parasolTestSupport)
ParasolTestSupport.ParasolLeaderThread (class in toil.test.batchSystems.parasolTestSupport)
ParasolTestSupport.ParasolThread (class in toil.test.batchSystems.parasolTestSupport)
ParasolTestSupport.ParasolWorkerThread (class in toil.test.batchSystems.parasolTestSupport)
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)
(in module tutorial_requirements)
parentMessage (in module toil.test.mesos.helloWorld)
parse_accelerator() (in module toil.job)
parse_accelerator_list() (in module toil.common)
parse_args() (in module toil.worker)
parse_bjobs_record() (toil.batchSystems.lsf.LSFBatchSystem.Worker method)
parse_cores() (in module toil.wdl.wdl_functions)
parse_declaration() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_declaration_expressn() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_declaration_expressn_arrayliteral() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_declaration_expressn_arraymaplookup() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_declaration_expressn_fncall() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_declaration_expressn_fncall_normalparams() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_declaration_expressn_logicalnot() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_declaration_expressn_memberaccess() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_declaration_expressn_operator() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_declaration_expressn_ternaryif() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_declaration_expressn_tupleliteral() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_declaration_name() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_declaration_type() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_disk() (in module toil.wdl.wdl_functions)
parse_elapsed() (toil.batchSystems.slurm.SlurmBatchSystem.Worker method)
parse_iso_utc() (in module toil.lib.memoize)
parse_mem_and_cmd_from_output() (in module toil.batchSystems.lsfHelper)
parse_memory() (in module toil.batchSystems.lsfHelper)
(in module toil.wdl.wdl_functions)
parse_memory_string() (in module toil.lib.conversions)
parse_node_types() (in module toil.provisioners)
parse_params() (toil.server.cli.wes_cwl_runner.WESClientWithWorkflowEngineParameters method)
parse_task() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_task_outputs() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_task_rawcommand() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_task_rawcommand_attributes() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_task_runtime() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_task_runtime_key() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_workflow() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_workflow_body() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_workflow_call() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_workflow_call_body() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_workflow_call_body_declarations() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_workflow_call_body_io() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_workflow_call_body_io_map() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_workflow_call_taskalias() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_workflow_call_taskname() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_workflow_if() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_workflow_if_expression() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_workflow_manifest_file() (in module toil.server.wes.amazon_wes_utils)
parse_workflow_scatter() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_workflow_scatter_collection() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
parse_workflow_scatter_item() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
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.Worker method)
parseBool() (in module toil.common)
parseDockerAppliance() (in module toil)
ParsedRequirement (in module toil.job)
parseLocator() (toil.common.Toil static method)
parseMaxMem() (toil.batchSystems.lsf.LSFBatchSystem.Worker method)
parseMemory() (in module toil.lib.ec2nodes)
parser (in module toil.test.provisioners.restartScript)
(in module tutorial_arguments)
(in module tutorial_helloworld)
(in module tutorial_multiplejobs)
(in module tutorial_multiplejobs2)
(in module tutorial_multiplejobs3)
parser_with_common_options() (in module toil.common)
parser_with_server_options() (in module toil.server.app)
parseSetEnv() (in module toil.common)
parseStorage() (in module toil.lib.ec2nodes)
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.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.singleMachine.SingleMachineBatchSystem attribute)
physicalMemory() (in module toil)
pick_value() (toil.cwl.cwltoil.ResolveSource method)
pickle() (toil.resource.Resource method)
pip() (toil.test.provisioners.clusterTest.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)
poll() (in module example_cachingbenchmark)
poll_run() (in module toil.server.cli.wes_cwl_runner)
populate_env_vars() (toil.cwl.cwltoil.CWLJob method)
potential_absolute_uris() (in module toil.wdl.wdltoil)
pre_update_hook() (toil.job.JobDescription method)
preemptable() (toil.job.Job method)
(toil.job.Requirer method)
preemptible (in module toil.test.batchSystems.batchSystemTest)
(toil.job.Job property)
(toil.job.RequirementsDict attribute)
(toil.job.Requirer property)
PreemptibleDeficitCompensationTest (class in toil.test.provisioners.aws.awsProvisionerTest)
PREFIX (toil.deferred.DeferredFunctionManager attribute)
PREFIX_LENGTH (in module toil.test.src.jobFileStoreTest)
prepare_restart() (toil.common.Config method)
prepare_start() (toil.common.Config method)
prepareBsub() (toil.batchSystems.lsf.LSFBatchSystem.Worker method)
prepareForPromiseRegistration() (toil.job.EncapsulatedJob method)
(toil.job.Job method)
prepareQsub() (toil.batchSystems.gridengine.GridEngineBatchSystem.Worker method)
(toil.batchSystems.torque.TorqueBatchSystem.Worker method)
prepareSbatch() (toil.batchSystems.slurm.SlurmBatchSystem.Worker method)
prepareSubmission() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.Worker method)
(toil.batchSystems.gridengine.GridEngineBatchSystem.Worker method)
(toil.batchSystems.htcondor.HTCondorBatchSystem.Worker method)
(toil.batchSystems.lsf.LSFBatchSystem.Worker method)
(toil.batchSystems.slurm.SlurmBatchSystem.Worker method)
(toil.batchSystems.torque.TorqueBatchSystem.Worker method)
prepareSystem() (toil.resource.Resource class method)
presenceIndicator() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo class method)
(toil.jobStores.aws.utils.SDBHelper class method)
prettyMemory() (in module toil.utils.toilStats)
prettyTime() (in module toil.utils.toilStats)
previousVersion (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo property)
primitive_types (toil.wdl.wdl_analysis.AnalyzeWDL attribute)
print_bus_messages() (toil.utils.toilStatus.ToilStatus method)
print_dot_chart() (toil.utils.toilStatus.ToilStatus method)
print_logs_and_exit() (in module toil.server.cli.wes_cwl_runner)
printAggregateJobStats() (toil.utils.toilStatus.ToilStatus method)
printContentsOfJobStore() (in module toil.utils.toilDebugFile)
printHelp() (in module toil.utils.toilMain)
printJobChildren() (toil.utils.toilStatus.ToilStatus method)
printJobLog() (toil.utils.toilStatus.ToilStatus method)
printq() (in module toil.lib.misc)
printUnicodeCharacter() (in module toil.test.utils.utilsTest)
printVersion() (in module toil.utils.toilMain)
process_and_read_file() (in module toil.wdl.wdl_functions)
process_finished_job() (toil.leader.Leader method)
process_finished_job_description() (toil.leader.Leader method)
process_infile() (in module toil.wdl.wdl_functions)
process_name_exists() (in module toil.lib.threading)
process_outfile() (in module toil.wdl.wdl_functions)
process_single_infile() (in module toil.wdl.wdl_functions)
process_single_outfile() (in module toil.wdl.wdl_functions)
processData() (in module toil.utils.toilStats)
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.job)
promise_tuples (toil.cwl.cwltoil.ResolveSource attribute)
Promised (in module toil.job)
PromisedRequirement (class in toil.job)
PromisedRequirementFunctionWrappingJob (class in toil.job)
PromisedRequirementJobFunctionWrappingJob (class in toil.job)
ProvisionerTest (class in toil.test.provisioners.provisionerTest)
ProxyConnectionError
prune() (in module toil.lib.ec2)
publicUrlExpiration (toil.jobStores.abstractJobStore.AbstractJobStore attribute)
publish() (toil.bus.MessageBus method)
(toil.bus.MessageOutbox method)
put_client() (toil.serviceManager.ServiceManager method)
putScript() (toil.test.provisioners.aws.awsProvisionerTest.AbstractAWSAutoscaleTest method)
python (in module toil.version)
python() (toil.test.provisioners.clusterTest.AbstractClusterTest method)
Q
queue_run() (toil.server.wes.toil_backend.ToilWorkflow method)
queue_size (toil.bus.QueueSizeMessage attribute)
QueueSizeMessage (class in toil.bus)
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)
reachable() (toil.test.src.jobTest.JobTest method)
read_boolean() (in module toil.wdl.wdl_functions)
read_cache() (toil.server.utils.AbstractStateStore method)
(toil.server.utils.WorkflowStateStore method)
read_csv() (in module toil.wdl.wdl_functions)
read_file() (in module toil.wdl.wdl_functions)
(toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
read_file_stream() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
read_float() (in module toil.wdl.wdl_functions)
read_from_url() (toil.jobStores.abstractJobStore.AbstractJobStore class method)
read_int() (in module toil.wdl.wdl_functions)
read_json() (in module toil.wdl.wdl_functions)
read_kill_flag() (toil.jobStores.abstractJobStore.AbstractJobStore method)
read_leader_node_id() (toil.jobStores.abstractJobStore.AbstractJobStore method)
read_leader_pid() (toil.jobStores.abstractJobStore.AbstractJobStore method)
read_lines() (in module toil.wdl.wdl_functions)
read_logs() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
read_map() (in module toil.wdl.wdl_functions)
read_shared_file_stream() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
read_single_file() (in module toil.wdl.wdl_functions)
read_string() (in module toil.wdl.wdl_functions)
read_tsv() (in module toil.wdl.wdl_functions)
ReadablePipe (class in toil.jobStores.utils)
ReadableTransformingPipe (class in toil.jobStores.utils)
readClusterSettings() (toil.provisioners.abstractProvisioner.AbstractProvisioner method)
(toil.provisioners.aws.awsProvisioner.AWSProvisioner method)
(toil.provisioners.gceProvisioner.GCEProvisioner method)
(toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method)
readFile() (toil.jobStores.abstractJobStore.AbstractJobStore method)
readFileStream() (toil.jobStores.abstractJobStore.AbstractJobStore method)
readFrom() (toil.jobStores.utils.WritablePipe method)
readGlobalFile() (toil.fileStores.abstractFileStore.AbstractFileStore method)
(toil.fileStores.cachingFileStore.CachingFileStore method)
(toil.fileStores.nonCachingFileStore.NonCachingFileStore method)
readGlobalFileStream() (toil.fileStores.abstractFileStore.AbstractFileStore method)
(toil.fileStores.cachingFileStore.CachingFileStore method)
(toil.fileStores.nonCachingFileStore.NonCachingFileStore method)
readSharedFileStream() (toil.jobStores.abstractJobStore.AbstractJobStore method)
readStatsAndLogging() (toil.jobStores.abstractJobStore.AbstractJobStore method)
readStatsFileOwnerID (toil.jobStores.aws.jobStore.AWSJobStore attribute)
realpath() (toil.cwl.cwltoil.ToilFsAccess method)
RealtimeLogger (class in toil.realtimeLogger)
RealtimeLoggerMetaclass (class in toil.realtimeLogger)
RealtimeLoggerTest (class in toil.test.src.realtimeLoggerTest)
recursive_dependencies() (in module toil.wdl.wdltoil)
refresh() (toil.resource.Resource method)
region (toil.test.server.serverTest.BucketUsingTest attribute)
region_to_bucket_location() (in module toil.lib.aws.utils)
regionDict (in module toil.lib.generatedEC2Lists)
register() (toil.resource.Resource method)
registered() (toil.batchSystems.mesos.batchSystem.MesosBatchSystem method)
(toil.batchSystems.mesos.executor.MesosExecutor method)
registerPromise() (toil.job.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)
remainingBillingInterval() (toil.provisioners.node.Node method)
(toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method)
remainingTryCount (toil.job.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.job.JobDescription method)
replace() (toil.job.JobDescription method)
replay_message_bus() (in module toil.bus)
report() (in module example_cachingbenchmark)
(toil.utils.toilStats.ColumnWidths method)
report_on_jobs() (toil.utils.toilStatus.ToilStatus method)
reportData() (in module toil.utils.toilStats)
reportMemory() (in module toil.utils.toilStats)
reportNumber() (in module toil.utils.toilStats)
reportPrettyData() (in module toil.utils.toilStats)
reportTime() (in module toil.utils.toilStats)
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.job.Requirer property)
requirements_string() (toil.job.Requirer method)
RequirementsDict (class in toil.job)
Requirer (class in toil.job)
reregistered() (toil.batchSystems.mesos.batchSystem.MesosBatchSystem method)
(toil.batchSystems.mesos.executor.MesosExecutor method)
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)
reset_job() (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)
resolveEntryPoint() (in module toil)
ResolveIndirect (class in toil.cwl.cwltoil)
ResolveSource (class in toil.cwl.cwltoil)
Resource (class in toil.resource)
resource() (in module toil.lib.aws.session)
(toil.lib.aws.session.AWSConnectionManager method)
resourceEnvNamePrefix (toil.resource.Resource attribute)
ResourceException
resourceOffers() (toil.batchSystems.mesos.batchSystem.MesosBatchSystem method)
ResourcePool (class in toil.batchSystems.abstractBatchSystem)
ResourceSet (class in toil.batchSystems.abstractBatchSystem)
ResourceTest (class in toil.test.src.resourceTest)
restart() (toil.common.Toil method)
restartCheckpoint() (toil.job.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)
result_status (toil.bus.JobUpdatedMessage attribute)
ResumabilityTest (class in toil.test.src.resumabilityTest)
resume() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
resumeJobStore() (toil.common.Toil class method)
retry() (in module toil)
(in module toil.batchSystems.mesos.test)
(in module toil.lib.retry)
retry_ec2() (in module toil.lib.ec2)
retry_flaky_test (in module toil.lib.retry)
retry_s3() (in module toil.lib.aws.utils)
retry_sdb() (in module toil.jobStores.aws.utils)
retryable_kubernetes_errors (in module toil.batchSystems.kubernetes)
retryable_s3_errors() (in module toil.lib.aws.utils)
retryable_sdb_errors() (in module toil.jobStores.aws.utils)
retryable_ssl_error() (in module toil.jobStores.aws.utils)
retryPredicate() (toil.provisioners.abstractProvisioner.AbstractProvisioner static method)
(toil.provisioners.aws.awsProvisioner.AWSProvisioner static method)
(toil.provisioners.gceProvisioner.GCEProvisioner 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)
rm_unprocessed_secondary_files() (in module toil.cwl.cwltoil)
robust_rmtree() (in module toil.lib.io)
root() (in module example_cachingbenchmark)
root_logger (in module toil.statsAndLogging)
rootDirPathEnvName (toil.resource.Resource attribute)
rootJobStoreIDFileName (toil.jobStores.abstractJobStore.AbstractJobStore attribute)
rsyncUtil() (toil.test.provisioners.aws.awsProvisionerTest.AbstractAWSAutoscaleTest method)
(toil.test.provisioners.gceProvisionerTest.AbstractGCEAutoscaleTest method)
run() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.Worker method)
(toil.batchSystems.mesos.test.ExceptionalThread 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.ResolveIndirect 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.leader.Leader method)
(toil.lib.threading.ExceptionalThread method)
(toil.server.wes.tasks.MultiprocessingTaskRunner class method)
(toil.server.wes.tasks.TaskRunner static method)
(toil.server.wes.tasks.ToilWorkflowRunner method)
(toil.test.batchSystems.parasolTestSupport.ParasolTestSupport.ParasolLeaderThread method)
(toil.test.batchSystems.parasolTestSupport.ParasolTestSupport.ParasolThread method)
(toil.test.ExceptionalThread method)
(toil.test.mesos.stress.HelloWorldFollowOn method)
(toil.test.mesos.stress.HelloWorldJob method)
(toil.test.mesos.stress.LongTestFollowOn method)
(toil.test.mesos.stress.LongTestJob 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.helloWorldTest.FollowOn method)
(toil.test.src.helloWorldTest.HelloWorld method)
(toil.test.src.importExportFileTest.RestartingJob method)
(toil.test.src.realtimeLoggerTest.LogTest method)
(toil.test.src.toilContextManagerTest.FollowOn method)
(toil.test.src.toilContextManagerTest.HelloWorld method)
(toil.test.src.userDefinedJobArgTypeTest.JobClass method)
(toil.test.utils.utilsTest.RunTwoJobsPerWorker method)
(toil.wdl.wdltoil.WDLArrayBindingsJob method)
(toil.wdl.wdltoil.WDLBaseJob method)
(toil.wdl.wdltoil.WDLCombineBindingsJob method)
(toil.wdl.wdltoil.WDLConditionalJob method)
(toil.wdl.wdltoil.WDLNamespaceBindingsJob method)
(toil.wdl.wdltoil.WDLOutputsJob method)
(toil.wdl.wdltoil.WDLRootJob method)
(toil.wdl.wdltoil.WDLScatterJob method)
(toil.wdl.wdltoil.WDLTaskJob method)
(toil.wdl.wdltoil.WDLWorkflowJob method)
(toil.wdl.wdltoil.WDLWorkflowNodeJob method)
(tutorial_arguments.HelloWorld method)
(tutorial_discoverfiles.discoverFiles method)
(tutorial_invokeworkflow.HelloWorld method)
(tutorial_invokeworkflow2.HelloWorld method)
(tutorial_managing.LocalFileStoreJob method)
(tutorial_staging.HelloWorld method)
run1000JobsOnMicros() (toil.test.provisioners.clusterScalerTest.BinPackingTest method)
run_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.common.Config attribute)
run_many() (fake_mpi_run.Runner method)
run_once() (fake_mpi_run.Runner method)
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.wes.abstract_backend.WESBackend method)
(toil.server.wes.toil_backend.ToilBackend method)
run_zip_workflow() (toil.test.server.serverTest.ToilWESServerWorkflowTest method)
runCheckpointVertexTest() (toil.test.src.jobTest.JobTest method)
runMain() (in module toil.test.sort.sortTest)
Runner (class in fake_mpi_run)
runNewCheckpointIsLeafVertexTest() (toil.test.src.jobTest.JobTest method)
running_on_ec2() (in module toil.lib.aws)
(in module toil.provisioners.aws)
(in module toil.test)
running_on_ecs() (in module toil.lib.aws)
runningPattern (toil.batchSystems.parasol.ParasolBatchSystem attribute)
runOnAppliance() (toil.test.ApplianceTestSupport.Appliance method)
runQC() (in module tutorial_cwlexample)
runToil() (toil.test.src.jobServiceTest.JobServiceTest method)
(toil.test.src.jobServiceTest.PerfectServiceTest method)
RunTwoJobsPerWorker (class in toil.test.utils.utilsTest)
rv() (toil.cwl.cwltoil.SelfJob method)
(toil.job.EncapsulatedJob method)
(toil.job.Job method)
S
s (in module tutorial_services)
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)
save() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo method)
save_batch_system_plugin_state() (in module toil.batchSystems.registry)
saveAsResourceTo() (toil.resource.ModuleDescriptor method)
saveAsRootJob() (toil.job.Job method)
saveBody() (toil.job.Job method)
(toil.job.ServiceHostJob method)
scale() (toil.job.Requirer method)
ScalerThread (class in toil.provisioners.clusterScaler)
ScalerThreadTest (class in toil.test.provisioners.clusterScalerTest)
scan_bus_messages() (toil.bus.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.utils)
SDBHelper (class in toil.jobStores.aws.utils)
secure_path() (toil.server.wes.abstract_backend.WESBackend static method)
select_first() (in module toil.wdl.wdl_functions)
SelfJob (class in toil.cwl.cwltoil)
send_cancel() (toil.server.utils.WorkflowStateMachine method)
send_canceled() (toil.server.utils.WorkflowStateMachine method)
send_complete() (toil.server.utils.WorkflowStateMachine method)
send_enqueue() (toil.server.utils.WorkflowStateMachine method)
send_executor_error() (toil.server.utils.WorkflowStateMachine method)
send_initialize() (toil.server.utils.WorkflowStateMachine method)
send_run() (toil.server.utils.WorkflowStateMachine method)
send_system_error() (toil.server.utils.WorkflowStateMachine method)
ServerSideCopyProhibitedError
serverThread (toil.realtimeLogger.RealtimeLogger attribute)
Service (class in toil.test.batchSystems.batchSystemTest)
serviceAccessor() (in module toil.test.src.jobServiceTest)
serviceHostIDsInBatches() (toil.job.JobDescription method)
ServiceHostJob (class in toil.job)
ServiceJobDescription (class in toil.job)
ServiceManager (class in toil.serviceManager)
services (toil.job.JobDescription property)
services_are_starting() (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)
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_config_defaults() (in module toil.batchSystems.options)
set_batchsystem_options() (in module toil.batchSystems.options)
set_log_level() (in module toil.statsAndLogging)
set_logging_from_options() (in module toil.statsAndLogging)
set_message_bus() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
(toil.batchSystems.abstractBatchSystem.BatchSystemSupport method)
set_preemptible() (toil.batchSystems.kubernetes.KubernetesBatchSystem.Placement method)
set_root_job() (toil.jobStores.abstractJobStore.AbstractJobStore method)
set_up_and_run_task() (toil.server.wes.tasks.MultiprocessingTaskRunner static method)
set_up_run() (toil.server.wes.toil_backend.ToilWorkflow method)
setAutoscaledNodeTypes() (toil.provisioners.abstractProvisioner.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.parasol.ParasolBatchSystem method)
setLoggingFromOptions() (in module toil.lib.bioio)
setNodeCount() (toil.provisioners.clusterScaler.ClusterScaler method)
setOptions() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem class method)
(toil.batchSystems.awsBatch.AWSBatchBatchSystem class method)
(toil.batchSystems.kubernetes.KubernetesBatchSystem class method)
(toil.batchSystems.mesos.batchSystem.MesosBatchSystem class method)
(toil.batchSystems.parasol.ParasolBatchSystem class method)
(toil.batchSystems.singleMachine.SingleMachineBatchSystem class method)
(toil.batchSystems.slurm.SlurmBatchSystem class method)
(toil.batchSystems.tes.TESBatchSystem class method)
(toil.common.Config method)
setRootJob() (toil.jobStores.abstractJobStore.AbstractJobStore method)
setStaticNodes() (toil.provisioners.clusterScaler.ClusterScaler method)
setup() (in module toil.test.sort.restart_sort)
(in module toil.test.sort.sort)
setUp() (toil.test.batchSystems.batchSystemTest.BatchSystemPluginTest method)
(toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemJobTest method)
(toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemTest method)
(toil.test.batchSystems.batchSystemTest.MaxCoresSingleMachineBatchSystemTest method)
(toil.test.batchSystems.test_slurm.SlurmTest method)
(toil.test.cwl.cwlTest.CWLOnARMTest method)
(toil.test.cwl.cwlTest.CWLv10Test method)
(toil.test.cwl.cwlTest.CWLWorkflowTest method)
(toil.test.jobStores.jobStoreTest.AbstractEncryptedJobStoreTest.Test method)
(toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method)
(toil.test.lib.dockerTest.DockerTest method)
(toil.test.lib.test_misc.UserNameUnvailableTest method)
(toil.test.lib.test_misc.UserNameVeryBrokenTest method)
(toil.test.provisioners.aws.awsProvisionerTest.AWSAutoscaleTest method)
(toil.test.provisioners.aws.awsProvisionerTest.AWSAutoscaleTestMultipleNodeTypes method)
(toil.test.provisioners.aws.awsProvisionerTest.AWSRestartTest method)
(toil.test.provisioners.aws.awsProvisionerTest.PreemptibleDeficitCompensationTest method)
(toil.test.provisioners.clusterScalerTest.BinPackingTest method)
(toil.test.provisioners.clusterScalerTest.ClusterScalerTest method)
(toil.test.provisioners.clusterTest.AbstractClusterTest method)
(toil.test.provisioners.gceProvisionerTest.AbstractGCEAutoscaleTest method)
(toil.test.provisioners.gceProvisionerTest.GCEAutoscaleTest method)
(toil.test.provisioners.gceProvisionerTest.GCEAutoscaleTestMultipleNodeTypes method)
(toil.test.provisioners.gceProvisionerTest.GCERestartTest method)
(toil.test.server.serverTest.AbstractToilWESServerTest method)
(toil.test.server.serverTest.FileStateStoreTest method)
(toil.test.server.serverTest.FileStateStoreURLTest method)
(toil.test.server.serverTest.ToilWESServerCeleryS3StateWorkflowTest method)
(toil.test.sort.sortTest.SortTest method)
(toil.test.src.autoDeploymentTest.AutoDeploymentTest method)
(toil.test.src.deferredFunctionTest.DeferredFunctionTest method)
(toil.test.src.fileStoreTest.hidden.AbstractCachingFileStoreTest method)
(toil.test.src.fileStoreTest.hidden.AbstractFileStoreTest method)
(toil.test.src.fileStoreTest.hidden.AbstractNonCachingFileStoreTest method)
(toil.test.src.importExportFileTest.ImportExportFileTest method)
(toil.test.src.jobDescriptionTest.JobDescriptionTest method)
(toil.test.src.miscTests.MiscTests method)
(toil.test.src.regularLogTest.RegularLogTest method)
(toil.test.src.restartDAGTest.RestartDAGTest method)
(toil.test.src.retainTempDirTest.CleanWorkDirTest method)
(toil.test.src.toilContextManagerTest.ToilContextManagerTest method)
(toil.test.src.userDefinedJobArgTypeTest.UserDefinedJobArgTypeTest method)
(toil.test.src.workerTest.WorkerTests method)
(toil.test.ToilTest method)
(toil.test.utils.toilKillTest.ToilKillTest method)
(toil.test.utils.utilsTest.UtilsTest method)
(toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest method)
(toil.test.wdl.toilwdlTest.BaseToilWdlTest method)
setup_method() (toil.test.ToilTest method)
setUpClass() (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemTest class method)
(toil.test.batchSystems.batchSystemTest.MaxCoresSingleMachineBatchSystemTest class method)
(toil.test.cwl.cwlTest.CWLv11Test class method)
(toil.test.cwl.cwlTest.CWLv12Test class method)
(toil.test.docs.scriptsTest.ToilDocumentationTest class method)
(toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test class method)
(toil.test.lib.aws.test_s3.S3Test class method)
(toil.test.lib.test_ec2.AMITest class method)
(toil.test.server.serverTest.BucketUsingTest class method)
(toil.test.src.jobTest.JobTest class method)
(toil.test.ToilTest class method)
(toil.test.wdl.builtinTest.WdlLanguageSpecWorkflowsTest class method)
(toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest class method)
(toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest class method)
(toil.test.wdl.builtinTest.WdlWorkflowsTest class method)
(toil.test.wdl.toilwdlTest.BaseToilWdlTest class method)
(toil.test.wdl.toilwdlTest.ToilWdlIntegrationTest class method)
(toil.test.wdl.wdltoil_test.ToilConformanceTests class method)
(toil.test.wdl.wdltoil_test.WdlToilTest class method)
setupJobAfterFailure() (toil.job.JobDescription method)
setUserScript() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
(toil.batchSystems.awsBatch.AWSBatchBatchSystem method)
(toil.batchSystems.kubernetes.KubernetesBatchSystem method)
(toil.batchSystems.mesos.batchSystem.MesosBatchSystem method)
(toil.batchSystems.tes.TESBatchSystem method)
setWidth() (toil.utils.toilStats.ColumnWidths method)
Shape (class in toil.batchSystems.mesos)
(class in toil.provisioners.abstractProvisioner)
shapes() (toil.provisioners.clusterScaler.NodeReservation method)
sharedFileNameRegex (toil.jobStores.abstractJobStore.AbstractJobStore attribute)
sharedFileOwnerID (toil.jobStores.aws.jobStore.AWSJobStore attribute)
shutdown() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
(toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem method)
(toil.batchSystems.awsBatch.AWSBatchBatchSystem method)
(toil.batchSystems.kubernetes.KubernetesBatchSystem method)
(toil.batchSystems.mesos.batchSystem.MesosBatchSystem method)
(toil.batchSystems.mesos.executor.MesosExecutor method)
(toil.batchSystems.parasol.ParasolBatchSystem method)
(toil.batchSystems.singleMachine.SingleMachineBatchSystem method)
(toil.batchSystems.tes.TESBatchSystem method)
(toil.common.ToilMetrics method)
(toil.fileStores.abstractFileStore.AbstractFileStore class method)
(toil.fileStores.cachingFileStore.CachingFileStore class method)
(toil.fileStores.nonCachingFileStore.NonCachingFileStore class method)
shutDown() (toil.provisioners.clusterScaler.ClusterScaler method)
shutdown() (toil.provisioners.clusterScaler.ScalerThread method)
(toil.serviceManager.ServiceManager method)
(toil.statsAndLogging.StatsAndLogging method)
shutDown() (toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method)
shutdownFileStore() (toil.fileStores.abstractFileStore.AbstractFileStore static method)
shutdownLocal() (toil.batchSystems.local_support.BatchSystemLocalSupport method)
shutDownStats() (toil.provisioners.clusterScaler.ClusterStats method)
simpleFileStoreJob() (in module toil.test.src.jobFileStoreTest)
simpleJobFn() (in module toil.test.src.jobTest)
simplify_list() (in module toil.cwl.cwltoil)
single_machine_batch_system_factory() (in module toil.batchSystems.registry)
SingleMachineBatchSystem (class in toil.batchSystems.singleMachine)
SingleMachineBatchSystemJobTest (class in toil.test.batchSystems.batchSystemTest)
SingleMachineBatchSystemTest (class in toil.test.batchSystems.batchSystemTest)
SingleMachinePromisedRequirementsTest (class in toil.test.src.promisedRequirementTest)
sitePackages (toil.test.src.autoDeploymentTest.AutoDeploymentTest attribute)
size() (in module toil.wdl.wdl_functions)
(toil.cwl.cwltoil.ToilFsAccess method)
SkipNull (class in toil.cwl.cwltoil)
skipped_outputs() (toil.cwl.cwltoil.Conditional method)
sleepSeconds() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem method)
sleepTime (toil.test.batchSystems.batchSystemTest.hidden.AbstractBatchSystemJobTest attribute)
slow() (in module toil.test)
slow_down() (in module toil.lib.misc)
slurm_batch_system_factory() (in module toil.batchSystems.registry)
SlurmBatchSystem (class in toil.batchSystems.slurm)
SlurmBatchSystem.Worker (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)
sort() (in module toil.test.sort.restart_sort)
(in module toil.test.sort.sort)
sort_category_choices (in module toil.utils.toilStats)
sort_field_choices (in module toil.utils.toilStats)
sort_options() (toil.server.wes.tasks.ToilWorkflowRunner method)
sortJobs() (in module toil.utils.toilStats)
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)
split() (in module toil.provisioners.clusterScaler)
sprintTag() (in module toil.utils.toilStats)
SQLITE_TIMEOUT_SECS (in module toil.fileStores.cachingFileStore)
sseKeyPath (toil.jobStores.aws.jobStore.AWSJobStore property)
sshAppliance() (toil.provisioners.node.Node method)
sshInstance() (toil.provisioners.node.Node method)
sshUtil() (toil.test.provisioners.clusterTest.AbstractClusterTest method)
(toil.test.provisioners.gceProvisionerTest.AbstractGCEAutoscaleTest method)
stageFn() (in module tutorial_requirements)
start() (toil.common.Toil method)
(toil.job.Job.Service method)
(toil.serviceManager.ServiceManager method)
(toil.statsAndLogging.StatsAndLogging method)
(toil.test.batchSystems.batchSystemTest.Service method)
(toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method)
(toil.test.src.jobServiceTest.ToySerializableService method)
(toil.test.src.jobServiceTest.ToyService method)
(toil.test.src.jobTest.TrivialService method)
(tutorial_services.DemoService method)
start_server() (in module toil.server.app)
startCommit() (toil.fileStores.abstractFileStore.AbstractFileStore method)
(toil.fileStores.cachingFileStore.CachingFileStore method)
(toil.fileStores.nonCachingFileStore.NonCachingFileStore method)
startCommitThread() (toil.fileStores.cachingFileStore.CachingFileStore method)
startDashboard() (toil.common.ToilMetrics method)
startStats() (toil.provisioners.clusterScaler.ClusterStats method)
startToil() (toil.job.Job.Runner static method)
STATE_DIR_STEM (toil.deferred.DeferredFunctionManager attribute)
state_store_cache (in module toil.server.utils)
STATE_TO_EXIT_REASON (in module toil.batchSystems.awsBatch)
(in module toil.batchSystems.tes)
StatsAndLogging (class in toil.statsAndLogging)
statsAndLoggingAggregator() (toil.statsAndLogging.StatsAndLogging class method)
statsCommand (toil.test.utils.utilsTest.UtilsTest property)
StatsDict (class in toil.worker)
statsFileOwnerID (toil.jobStores.aws.jobStore.AWSJobStore attribute)
statusCommand() (toil.test.utils.utilsTest.UtilsTest method)
statusUpdate() (toil.batchSystems.mesos.batchSystem.MesosBatchSystem method)
StepValueFrom (class in toil.cwl.cwltoil)
STOP (in module toil.lib.docker)
stop() (toil.job.Job.Service method)
(toil.test.batchSystems.batchSystemTest.Service method)
(toil.test.src.jobServiceTest.ToySerializableService method)
(toil.test.src.jobServiceTest.ToyService method)
(toil.test.src.jobTest.TrivialService method)
(tutorial_services.DemoService method)
streamingFileStoreString (in module toil.test.src.jobFileStoreTest)
strict_bool() (in module toil.lib.memoize)
StubHttpRequestHandler (class in toil.test.jobStores.jobStoreTest)
sub() (in module toil.wdl.wdl_functions)
submit_run() (in module toil.server.cli.wes_cwl_runner)
submitJob() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.Worker method)
(toil.batchSystems.gridengine.GridEngineBatchSystem.Worker method)
(toil.batchSystems.htcondor.HTCondorBatchSystem.Worker method)
(toil.batchSystems.lsf.LSFBatchSystem.Worker method)
(toil.batchSystems.slurm.SlurmBatchSystem.Worker method)
(toil.batchSystems.torque.TorqueBatchSystem.Worker method)
subprocessDockerCall() (in module toil.lib.docker)
subscribe() (toil.bus.MessageBus method)
subtract() (toil.provisioners.clusterScaler.NodeReservation method)
successor_returned() (toil.toilState.ToilState method)
successors_by_phase() (toil.job.JobDescription method)
successors_pending() (toil.toilState.ToilState method)
successorsAndServiceHosts() (toil.job.JobDescription method)
SUPPORTED_HTTP_ERRORS (in module toil.lib.retry)
supportedClusterTypes() (toil.provisioners.abstractProvisioner.AbstractProvisioner method)
(toil.provisioners.aws.awsProvisioner.AWSProvisioner method)
(toil.provisioners.gceProvisioner.GCEProvisioner 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.kubernetes.KubernetesBatchSystem class method)
(toil.batchSystems.mesos.batchSystem.MesosBatchSystem class method)
(toil.batchSystems.parasol.ParasolBatchSystem class method)
(toil.batchSystems.singleMachine.SingleMachineBatchSystem class method)
(toil.batchSystems.tes.TESBatchSystem 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.ParasolBatchSystemTest method)
(toil.test.batchSystems.batchSystemTest.SingleMachineBatchSystemTest method)
(toil.test.batchSystems.batchSystemTest.TESBatchSystemTest method)
supportsWorkerCleanup() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem class method)
(toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem class method)
(toil.batchSystems.cleanup_support.BatchSystemCleanupSupport class method)
(toil.batchSystems.mesos.batchSystem.MesosBatchSystem class method)
(toil.batchSystems.parasol.ParasolBatchSystem class method)
(toil.batchSystems.singleMachine.SingleMachineBatchSystem class method)
suppress_exotic_logging() (in module toil.statsAndLogging)
sync_memoize() (in module toil.lib.memoize)
SynthesizeWDL (class in toil.wdl.wdl_synthesis)
SYS_MAX_SIZE (in module toil.common)
system() (in module toil.lib.bioio)
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)
task_filter() (in module toil.server.wes.amazon_wes_utils)
TaskData (in module toil.batchSystems.mesos)
TaskLog (in module toil.server.wes.abstract_backend)
TaskRunner (class in toil.server.wes.tasks)
tearDown() (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.ParasolBatchSystemTest method)
(toil.test.batchSystems.batchSystemTest.SlurmBatchSystemTest method)
(toil.test.batchSystems.batchSystemTest.TorqueBatchSystemTest 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.docs.scriptsTest.ToilDocumentationTest method)
(toil.test.jobStores.jobStoreTest.AbstractEncryptedJobStoreTest.Test method)
(toil.test.jobStores.jobStoreTest.AbstractJobStoreTest.Test method)
(toil.test.lib.test_misc.UserNameUnvailableTest method)
(toil.test.lib.test_misc.UserNameVeryBrokenTest method)
(toil.test.provisioners.clusterTest.AbstractClusterTest method)
(toil.test.provisioners.gceProvisionerTest.AbstractGCEAutoscaleTest method)
(toil.test.server.serverTest.AbstractToilWESServerTest method)
(toil.test.sort.sortTest.SortTest method)
(toil.test.src.jobDescriptionTest.JobDescriptionTest method)
(toil.test.src.promisedRequirementTest.MesosPromisedRequirementsTest method)
(toil.test.src.promisedRequirementTest.SingleMachinePromisedRequirementsTest method)
(toil.test.src.restartDAGTest.RestartDAGTest method)
(toil.test.src.retainTempDirTest.CleanWorkDirTest method)
(toil.test.src.toilContextManagerTest.ToilContextManagerTest method)
(toil.test.ToilTest method)
(toil.test.utils.toilKillTest.ToilKillTest method)
(toil.test.utils.utilsTest.UtilsTest method)
(toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest method)
(toil.test.wdl.toilwdlTest.BaseToilWdlTest method)
tearDownClass() (toil.test.lib.aws.test_s3.S3Test class method)
(toil.test.server.serverTest.BucketUsingTest class method)
(toil.test.ToilTest class method)
(toil.test.wdl.toilwdlTest.ToilWdlIntegrationTest class method)
(toil.test.wdl.wdltoil_test.ToilConformanceTests class method)
tearDownModule() (in module toil.test.jobStores.jobStoreTest)
tempDir (toil.job.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)
TERMINAL_STATES (in module toil.server.utils)
terminateNodes() (toil.provisioners.abstractProvisioner.AbstractProvisioner method)
(toil.provisioners.aws.awsProvisioner.AWSProvisioner method)
(toil.provisioners.gceProvisioner.GCEProvisioner method)
(toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method)
tes_batch_system_factory() (in module toil.batchSystems.registry)
tes_bearer_token (toil.common.Config attribute)
tes_endpoint (toil.common.Config attribute)
tes_password (toil.common.Config attribute)
tes_user (toil.common.Config attribute)
TESBatchSystem (class in toil.batchSystems.tes)
TESBatchSystemTest (class in toil.test.batchSystems.batchSystemTest)
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_AMI_finding() (toil.test.provisioners.aws.awsProvisionerTest.AWSProvisionerBenchTest method)
test_as_map() (toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest method)
test_as_pairs() (toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest 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_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_bypass_stable_feed() (toil.test.lib.test_ec2.FlatcarFeedTest method)
test_call_command_err() (toil.test.src.miscTests.MiscTests method)
test_call_command_ok() (toil.test.src.miscTests.MiscTests method)
test_ceil() (toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest 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_collect_by_key() (toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest method)
test_conformance_tests_v10() (toil.test.wdl.wdltoil_test.ToilConformanceTests method)
test_conformance_tests_v11() (toil.test.wdl.wdltoil_test.ToilConformanceTests method)
test_convert() (toil.test.lib.test_conversions.ConversionTest method)
test_create_bucket() (toil.test.lib.aws.test_s3.S3Test method)
test_cross() (toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest method)
test_cross_thread_messaging() (toil.test.src.busTest.MessageBusTest method)
test_cuda() (toil.test.cwl.cwlTest.CWLWorkflowTest method)
test_cwl_on_arm() (toil.test.cwl.cwlTest.CWLOnARMTest method)
test_cwl_toil_kill() (toil.test.utils.toilKillTest.ToilKillTest method)
test_download_directory_file() (toil.test.cwl.cwlTest.CWLWorkflowTest method)
test_download_directory_s3() (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_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_empty_file_path() (toil.test.wdl.wdltoil_test.WdlToilTest method)
,
[1]
test_enum_ints_in_file() (toil.test.src.busTest.MessageBusTest 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_flatten() (toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest method)
test_floor() (toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest method)
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.WdlToilTest method)
test_giraffe_deepvariant() (toil.test.wdl.wdltoil_test.WdlToilTest 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.WdlToilTest 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_keys() (toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest 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_length() (toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest 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_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.WdlToilTest 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_parasol_cwl_conformance() (toil.test.cwl.cwlTest.CWLv10Test method)
test_parasol_cwl_conformance_with_caching() (toil.test.cwl.cwlTest.CWLv10Test 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_range() (toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest method)
test_read() (toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest 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_round() (toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest 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_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_size() (toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest method)
test_size_large() (toil.test.wdl.toilwdlTest.ToilWdlIntegrationTest 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_stdout() (toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest method)
test_streamable() (toil.test.cwl.cwlTest.CWLWorkflowTest method)
test_sub() (toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest method)
test_torque_cwl_conformance() (toil.test.cwl.cwlTest.CWLv10Test method)
test_torque_cwl_conformance_with_caching() (toil.test.cwl.cwlTest.CWLv10Test method)
test_transpose() (toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest method)
test_type_pair() (toil.test.wdl.builtinTest.WdlLanguageSpecWorkflowsTest method)
test_usage_message() (in module toil.test.cwl.cwlTest)
test_v1_declaration() (toil.test.wdl.builtinTest.WdlLanguageSpecWorkflowsTest 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_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_write() (toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest method)
test_zip() (toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest method)
testAddBatchSystemFactory() (toil.test.batchSystems.batchSystemTest.BatchSystemPluginTest method)
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)
testBatchResourceLimits() (toil.test.batchSystems.batchSystemTest.ParasolBatchSystemTest 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)
testCSV() (toil.test.wdl.toilwdlTest.ToilWDLLibraryTest method)
testCwlexample() (toil.test.docs.scriptsTest.ToilDocumentationTest 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)
testDiscoverfiles() (toil.test.docs.scriptsTest.ToilDocumentationTest 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)
testENCODE() (toil.test.wdl.toilwdlTest.ToilWdlIntegrationTest method)
testEncrypted() (toil.test.jobStores.jobStoreTest.AbstractEncryptedJobStoreTest.Test method)
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)
testFetchJobStoreFilesWSymlinks() (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)
testFileParasol() (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)
testFn_Basename() (toil.test.wdl.toilwdlTest.ToilWDLLibraryTest method)
testFn_Ceil() (toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest method)
testFn_Cross() (toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest method)
testFn_Floor() (toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest method)
testFn_Glob() (toil.test.wdl.toilwdlTest.ToilWDLLibraryTest method)
testFn_Length() (toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest method)
testFn_ParseCores() (toil.test.wdl.toilwdlTest.ToilWDLLibraryTest method)
testFn_ParseDisk() (toil.test.wdl.toilwdlTest.ToilWDLLibraryTest method)
testFn_ParseMemory() (toil.test.wdl.toilwdlTest.ToilWDLLibraryTest method)
testFn_ReadBoolean() (toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest method)
testFn_ReadFloat() (toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest method)
testFn_ReadInt() (toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest method)
testFn_ReadJson() (toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest method)
testFn_ReadLines() (toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest method)
testFn_ReadMap() (toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest method)
testFn_ReadString() (toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest method)
testFn_ReadTsv() (toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest method)
testFn_SelectFirst() (toil.test.wdl.toilwdlTest.ToilWDLLibraryTest method)
testFn_Size() (toil.test.wdl.toilwdlTest.ToilWDLLibraryTest method)
testFn_Sub() (toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest method)
testFn_Transpose() (toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest method)
testFn_WriteJson() (toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest method)
testFn_WriteLines() (toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest method)
testFn_WriteMap() (toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest method)
testFn_WriteTsv() (toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest method)
testFn_Zip() (toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest 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)
testJSON() (toil.test.wdl.toilwdlTest.ToilWdlIntegrationTest 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)
testMD5sum() (toil.test.wdl.toilwdlTest.ToilWdlTest method)
(toil.test.wdl.wdltoil_test.WdlToilTest 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)
testPipe() (toil.test.wdl.toilwdlTest.ToilWdlIntegrationTest method)
testPreemptibleDeficitIsSet() (toil.test.provisioners.clusterScalerTest.ClusterScalerTest method)
testPreemptibleDeficitResponse() (toil.test.provisioners.clusterScalerTest.ClusterScalerTest method)
testPreserveFileName() (toil.test.jobStores.jobStoreTest.FileJobStoreTest method)
testPrimitives() (toil.test.wdl.toilwdlTest.ToilWDLLibraryTest 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)
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)
testTSV() (toil.test.wdl.toilwdlTest.ToilWDLLibraryTest method)
testTut01() (toil.test.wdl.toilwdlTest.ToilWdlIntegrationTest method)
testTut02() (toil.test.wdl.toilwdlTest.ToilWdlIntegrationTest method)
testTut03() (toil.test.wdl.toilwdlTest.ToilWdlIntegrationTest method)
testTut04() (toil.test.wdl.toilwdlTest.ToilWdlIntegrationTest 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)
ThreadingTest (class in toil.test.src.threadingTest)
throttle (class in toil.lib.throttle)
throttle() (toil.lib.throttle.LocalThrottle method)
THROTTLED_ERROR_CODES (in module toil.lib.aws.utils)
timeLimit() (in module toil.test)
title() (toil.utils.toilStats.ColumnWidths method)
to_dict() (toil.wdl.wdl_types.WDLPair method)
toCommand() (toil.resource.ModuleDescriptor method)
toIgnitionConfig() (toil.provisioners.abstractProvisioner.AbstractProvisioner.InstanceConfiguration method)
toil
module
Toil (class in toil.common)
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.parasol
module
toil.batchSystems.registry
module
toil.batchSystems.singleMachine
module
toil.batchSystems.slurm
module
toil.batchSystems.tes
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._dummy
module
toil.lib.encryption._nacl
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.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.batchSystemTest
module
toil.test.batchSystems.parasolTestSupport
module
toil.test.batchSystems.test_lsf_helper
module
toil.test.batchSystems.test_slurm
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.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.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.builtinTest
module
toil.test.wdl.conftest
module
toil.test.wdl.toilwdlTest
module
toil.test.wdl.wdltoil_test
module
toil.toilState
module
toil.utils
module
toil.utils.toilClean
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.toilwdl
module
toil.wdl.utils
module
toil.wdl.versions
module
toil.wdl.versions.dev
module
toil.wdl.versions.draft2
module
toil.wdl.versions.v1
module
toil.wdl.wdl_analysis
module
toil.wdl.wdl_functions
module
toil.wdl.wdl_synthesis
module
toil.wdl.wdl_types
module
toil.wdl.wdltoil
module
toil.worker
module
toil_batch_id (toil.bus.ExternalBatchIdMessage attribute)
(toil.bus.JobIssuedMessage attribute)
(toil.bus.JobStatus attribute)
toil_get_file() (in module toil.cwl.cwltoil)
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.provisioners.abstractProvisioner.AbstractProvisioner method)
(toil.provisioners.aws.awsProvisioner.AWSProvisioner method)
TOIL_URI_SCHEME (in module toil.wdl.wdltoil)
ToilBackend (class in toil.server.wes.toil_backend)
ToilCommandLineTool (class in toil.cwl.cwltoil)
ToilConformanceTests (class in toil.test.wdl.wdltoil_test)
ToilContextManagerException
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)
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)
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.toilState)
ToilStatus (class in toil.utils.toilStatus)
ToilTest (class in toil.test)
ToilTool (class in toil.cwl.cwltoil)
ToilWdlIntegrationTest (class in toil.test.wdl.toilwdlTest)
ToilWDLLibraryTest (class in toil.test.wdl.toilwdlTest)
ToilWDLStdLibBase (class in toil.wdl.wdltoil)
ToilWDLStdLibTaskCommand (class in toil.wdl.wdltoil)
ToilWDLStdLibTaskOutputs (class in toil.wdl.wdltoil)
ToilWdlTest (class in toil.test.wdl.toilwdlTest)
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)
tokenize_conf_stream() (in module toil.batchSystems.lsfHelper)
tolerated_taints (toil.batchSystems.kubernetes.KubernetesBatchSystem.Placement attribute)
torque_batch_system_factory() (in module toil.batchSystems.registry)
TorqueBatchSystem (class in toil.batchSystems.torque)
TorqueBatchSystem.Worker (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.utils.ReadableTransformingPipe method)
translate_wdl_string_to_python_string() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
transpose() (in module toil.wdl.wdl_functions)
traverseJobGraph() (toil.utils.toilStatus.ToilStatus method)
trivialParent() (in module toil.test.src.jobTest)
TrivialService (class in toil.test.src.jobTest)
truncExpBackoff() (in module toil.lib.misc)
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.lib.io)
tryRun() (toil.batchSystems.mesos.test.ExceptionalThread method)
(toil.batchSystems.mesos.test.MesosTestSupport.MesosThread method)
(toil.lib.threading.ExceptionalThread method)
(toil.provisioners.clusterScaler.ScalerThread method)
(toil.test.ApplianceTestSupport.Appliance method)
(toil.test.ExceptionalThread method)
tutorial_arguments
module
tutorial_cwlexample
module
tutorial_discoverfiles
module
tutorial_docker
module
tutorial_dynamic
module
tutorial_encapsulation
module
tutorial_encapsulation2
module
tutorial_helloworld
module
tutorial_invokeworkflow
module
tutorial_invokeworkflow2
module
tutorial_jobfunctions
module
tutorial_managing
module
tutorial_managing2
module
tutorial_multiplejobs
module
tutorial_multiplejobs2
module
tutorial_multiplejobs3
module
tutorial_promises
module
tutorial_promises2
module
tutorial_quickstart
module
tutorial_requirements
module
tutorial_services
module
tutorial_staging
module
typeEmpty() (toil.batchSystems.mesos.JobQueue method)
U
UnexpectedResourceState
UnfulfilledPromiseSentinel (class in toil.job)
unignoreNode() (toil.batchSystems.abstractBatchSystem.AbstractScalableBatchSystem method)
(toil.batchSystems.mesos.batchSystem.MesosBatchSystem method)
(toil.test.provisioners.clusterScalerTest.MockBatchSystemAndProvisioner method)
UnimplementedURLException
unix_now_ms() (in module toil.lib.misc)
unpack() (toil.fileStores.FileID class method)
unpack_toil_uri() (in module toil.wdl.wdltoil)
unpickle() (toil.resource.Resource class method)
UnresolvedDict (class in toil.cwl.cwltoil)
unwrap() (in module toil.job)
unwrap_all() (in module toil.job)
up() (in module toil.test.sort.restart_sort)
(in module toil.test.sort.sort)
update() (toil.jobStores.abstractJobStore.AbstractJobStore method)
update_file() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
update_file_stream() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
update_job() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
updateClusterSize() (toil.provisioners.clusterScaler.ClusterScaler method)
updateColumnWidths() (in module toil.utils.toilStats)
UpdatedBatchJobInfo (class in toil.batchSystems.abstractBatchSystem)
updatedJobWorker() (toil.batchSystems.parasol.ParasolBatchSystem method)
updateFile() (toil.jobStores.abstractJobStore.AbstractJobStore method)
updateFileStream() (toil.jobStores.abstractJobStore.AbstractJobStore method)
updateStaticEC2Instances() (in module toil.lib.ec2nodes)
upload() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo method)
upload_directory() (in module toil.cwl.cwltoil)
upload_file() (in module toil.cwl.cwltoil)
uploadFile() (in module toil.jobStores.aws.utils)
uploadFromPath() (in module toil.jobStores.aws.utils)
uploadStream() (toil.jobStores.aws.jobStore.AWSJobStore.FileInfo method)
UpReturnType (in module toil.cwl.utils)
usage_message (in module toil.cwl.cwltoil)
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.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.jobStores.fileJobStore.FileJobStore attribute)
validDirsSet (toil.jobStores.fileJobStore.FileJobStore attribute)
version (in module toil.version)
(toil.jobStores.aws.jobStore.AWSJobStore.FileInfo property)
(toil.wdl.versions.dev.AnalyzeDevelopmentWDL property)
(toil.wdl.versions.draft2.AnalyzeDraft2WDL property)
(toil.wdl.versions.v1.AnalyzeV1WDL property)
(toil.wdl.wdl_analysis.AnalyzeWDL property)
versionings (toil.jobStores.aws.jobStore.AWSJobStore attribute)
VersionNotImplementedException
VirtualEnvResource (class in toil.resource)
virtualize_files() (in module toil.wdl.wdltoil)
visit() (toil.cwl.cwltoil.ToilPathMapper method)
visit_any_decls() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_apply() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_array_literal() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_at() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_bound_decls() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_call() (toil.wdl.versions.dev.AnalyzeDevelopmentWDL method)
(toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_conditional() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_cwl_class_and_reduce() (in module toil.cwl.utils)
visit_document() (toil.wdl.versions.dev.AnalyzeDevelopmentWDL method)
(toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_document_element() (toil.wdl.versions.dev.AnalyzeDevelopmentWDL method)
(toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_expr() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_expr_core() (toil.wdl.versions.dev.AnalyzeDevelopmentWDL method)
(toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_expression_group() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_expression_placeholder_option() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_get_name() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_ifthenelse() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_infix0() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_infix1() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_infix2() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_infix3() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_infix4() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_infix5() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_inner_workflow_element() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_land() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_lor() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_negate() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_number() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_pair_literal() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_primitive_literal() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_primitives() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_scatter() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_string() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_string_expr_part() (toil.wdl.versions.dev.AnalyzeDevelopmentWDL method)
(toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_string_expr_with_string_part() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_string_part() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_task() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_task_command() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_task_command_expr_part() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_task_command_expr_with_string() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_task_command_string_part() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_task_input() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_task_output() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_task_runtime() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_top_cwl_class() (in module toil.cwl.utils)
visit_unarysigned() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_unbound_decls() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_wdl_type() (toil.wdl.versions.dev.AnalyzeDevelopmentWDL method)
(toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_workflow() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_workflow_input() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visit_workflow_output() (toil.wdl.versions.v1.AnalyzeV1WDL method)
visitSteps() (in module toil.cwl.cwltoil)
W
WAIT_FOR_DEATH_TIMEOUT (in module toil.server.wes.tasks)
wait_for_master() (toil.batchSystems.mesos.test.MesosTestSupport method)
wait_instances_running() (in module toil.lib.ec2)
wait_spot_requests_active() (in module toil.lib.ec2)
wait_transition() (in module toil.lib.ec2)
wait_until_instance_profile_arn_exists() (in module toil.lib.ec2)
waitForCommit() (toil.fileStores.abstractFileStore.AbstractFileStore method)
(toil.fileStores.cachingFileStore.CachingFileStore method)
(toil.fileStores.nonCachingFileStore.NonCachingFileStore method)
waitForNode() (toil.provisioners.node.Node method)
wallTime (toil.batchSystems.abstractBatchSystem.UpdatedBatchJobInfo attribute)
wdl_data (toil.test.wdl.toilwdlTest.ToilWdlIntegrationTest attribute)
wdl_data_dir (toil.test.wdl.toilwdlTest.ToilWdlIntegrationTest attribute)
wdl_dir (toil.test.wdl.wdltoil_test.ToilConformanceTests attribute)
wdl_range() (in module toil.wdl.wdl_functions)
wdl_zip() (in module toil.wdl.wdl_functions)
WDLArrayBindingsJob (class in toil.wdl.wdltoil)
WDLArrayType (class in toil.wdl.wdl_types)
WDLBaseJob (class in toil.wdl.wdltoil)
WDLBindings (in module toil.wdl.wdltoil)
WDLBooleanType (class in toil.wdl.wdl_types)
WDLCombineBindingsJob (class in toil.wdl.wdltoil)
WDLCompoundType (class in toil.wdl.wdl_types)
WDLConditionalJob (class in toil.wdl.wdltoil)
WDLFile (class in toil.wdl.wdl_types)
WDLFileType (class in toil.wdl.wdl_types)
WDLFloatType (class in toil.wdl.wdl_types)
WDLIntType (class in toil.wdl.wdl_types)
WDLJSONEncoder (class in toil.wdl.wdl_functions)
WdlLanguageSpecWorkflowsTest (class in toil.test.wdl.builtinTest)
WDLMapType (class in toil.wdl.wdl_types)
WDLNamespaceBindingsJob (class in toil.wdl.wdltoil)
WDLOutputsJob (class in toil.wdl.wdltoil)
WDLPair (class in toil.wdl.wdl_types)
WDLPairType (class in toil.wdl.wdl_types)
WDLRootJob (class in toil.wdl.wdltoil)
WDLRuntimeError
,
[1]
WDLScatterJob (class in toil.wdl.wdltoil)
WDLSectionJob (class in toil.wdl.wdltoil)
WdlStandardLibraryFunctionsTest (class in toil.test.wdl.builtinTest)
WdlStandardLibraryWorkflowsTest (class in toil.test.wdl.builtinTest)
WDLStringType (class in toil.wdl.wdl_types)
WDLTaskJob (class in toil.wdl.wdltoil)
WdlToilTest (class in toil.test.wdl.wdltoil_test)
WDLType (class in toil.wdl.wdl_types)
WDLWorkflowJob (class in toil.wdl.wdltoil)
WDLWorkflowNodeJob (class in toil.wdl.wdltoil)
WdlWorkflowsTest (class in toil.test.wdl.builtinTest)
WESBackend (class in toil.server.wes.abstract_backend)
WESClientWithWorkflowEngineParameters (class in toil.server.cli.wes_cwl_runner)
which() (in module toil)
WIP_SUFFIX (toil.deferred.DeferredFunctionManager attribute)
with_retries() (toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem method)
work_dir (toil.batchSystems.abstractBatchSystem.WorkerCleanupInfo attribute)
workerCleanup() (toil.batchSystems.abstractBatchSystem.BatchSystemSupport static method)
WorkerCleanupContext (class in toil.batchSystems.cleanup_support)
WorkerCleanupInfo (class in toil.batchSystems.abstractBatchSystem)
workerScript() (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)
workflow_manifest_url_to_path() (in module toil.server.wes.amazon_wes_utils)
workflowAttemptNumber (toil.common.Config attribute)
WorkflowConflictException
workflowDependencies (toil.server.wes.amazon_wes_utils.FilesDict attribute)
WorkflowExecutionException
workflowID (toil.common.Config attribute)
workflowInputFiles (toil.server.wes.amazon_wes_utils.FilesDict attribute)
WorkflowNotFoundException
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)
WorkflowStateStore (class in toil.server.utils)
workflowUrl (toil.server.wes.amazon_wes_utils.DataDict attribute)
wrapFn() (toil.job.Job static method)
wrapJobFn() (toil.job.Job static method)
WritablePipe (class in toil.jobStores.utils)
write() (toil.lib.io.WriteWatchingStream method)
write_AST() (toil.wdl.versions.draft2.AnalyzeDraft2WDL method)
(toil.wdl.wdl_analysis.AnalyzeWDL method)
write_cache() (toil.server.utils.AbstractStateStore method)
(toil.server.utils.WorkflowStateStore method)
write_config() (toil.jobStores.abstractJobStore.AbstractJobStore method)
write_declaration_type() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_file() (in module toil.cwl.cwltoil)
(toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
write_file_stream() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
write_function() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_function_bashscriptline() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_function_cmdline() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_function_dockercall() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_function_header() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_function_outputreturn() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_function_subprocesspopen() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_functions() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_json() (in module toil.wdl.wdl_functions)
write_kill_flag() (toil.jobStores.abstractJobStore.AbstractJobStore method)
write_leader_node_id() (toil.jobStores.abstractJobStore.AbstractJobStore method)
write_leader_pid() (toil.jobStores.abstractJobStore.AbstractJobStore method)
write_lines() (in module toil.wdl.wdl_functions)
write_logs() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
write_main() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_main_destbucket() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_main_header() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_main_jobwrappers() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_main_jobwrappers_call() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_main_jobwrappers_declaration() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_main_jobwrappers_if() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_main_jobwrappers_scatter() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_map() (in module toil.wdl.wdl_functions)
write_mappings() (in module toil.wdl.utils)
write_modules() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_output_files() (toil.server.wes.tasks.ToilWorkflowRunner method)
write_python_file() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_scatter_callwrapper() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_scatterfunction() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_scatterfunction_header() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_scatterfunction_lists() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_scatterfunction_loop() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_scatterfunction_outputreturn() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_scatterfunctions_within_if() (toil.wdl.wdl_synthesis.SynthesizeWDL method)
write_scratch_file() (toil.server.wes.tasks.ToilWorkflowRunner method)
write_shared_file_stream() (toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.aws.jobStore.AWSJobStore method)
(toil.jobStores.fileJobStore.FileJobStore method)
(toil.jobStores.googleJobStore.GoogleJobStore method)
write_temp_file() (in module toil.test.batchSystems.batchSystemTest)
write_tsv() (in module toil.wdl.wdl_functions)
write_workflow() (toil.server.wes.tasks.ToilWorkflowRunner method)
writeA() (in module debugWorkflow)
writeABC() (in module debugWorkflow)
writeB() (in module debugWorkflow)
writeC() (in module debugWorkflow)
writeConfig() (toil.jobStores.abstractJobStore.AbstractJobStore method)
writeFile() (toil.jobStores.abstractJobStore.AbstractJobStore method)
writeFileStream() (toil.jobStores.abstractJobStore.AbstractJobStore method)
writeGlobalFile() (toil.fileStores.abstractFileStore.AbstractFileStore method)
(toil.fileStores.cachingFileStore.CachingFileStore method)
(toil.fileStores.nonCachingFileStore.NonCachingFileStore method)
writeGlobalFileStream() (toil.fileStores.abstractFileStore.AbstractFileStore method)
writeGlobalFileWrapper() (in module toil.cwl.cwltoil)
writelines() (toil.lib.io.WriteWatchingStream method)
writeLogFiles() (toil.statsAndLogging.StatsAndLogging class method)
writeSharedFileStream() (toil.jobStores.abstractJobStore.AbstractJobStore method)
writeStatsAndLogging() (toil.jobStores.abstractJobStore.AbstractJobStore method)
writeTo() (toil.jobStores.utils.ReadablePipe method)
(toil.jobStores.utils.ReadableTransformingPipe method)
writeToAppliance() (toil.test.ApplianceTestSupport.Appliance method)
WriteWatchingStream (class in toil.lib.io)
Z
zone_to_region() (in module toil.lib.aws)
(in module toil.provisioners.aws)
ZoneTuple (in module toil.provisioners.aws)
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