Index
_
|
A
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
W
_
__init__() (toil.common.Toil method)
(toil.fileStore.FileStore method)
(toil.job.EncapsulatedJob method)
(toil.job.FunctionWrappingJob method)
(toil.job.Job method)
(toil.job.Job.Service method)
(toil.job.JobException method)
(toil.job.JobGraphDeadlockException method)
(toil.job.Promise method)
(toil.job.PromisedRequirement method)
(toil.jobStores.abstractJobStore.AbstractJobStore method)
(toil.jobStores.abstractJobStore.ConcurrentFileModificationException method)
(toil.jobStores.abstractJobStore.JobStoreExistsException method)
(toil.jobStores.abstractJobStore.NoSuchFileException method)
(toil.jobStores.abstractJobStore.NoSuchJobException method)
(toil.jobStores.abstractJobStore.NoSuchJobStoreException method)
A
AbstractBatchSystem (class in toil.batchSystems.abstractBatchSystem)
AbstractJobStore (class in toil.jobStores.abstractJobStore)
addChild() (toil.job.Job method)
addChildFn() (toil.job.Job method)
addChildJobFn() (toil.job.Job method)
addFollowOn() (toil.job.Job method)
addFollowOnFn() (toil.job.Job method)
addFollowOnJobFn() (toil.job.Job method)
addService() (toil.job.Job method)
addToilOptions() (toil.job.Job.Runner static method)
C
check() (toil.job.Job.Service method)
checkJobGraphAcylic() (toil.job.Job method)
checkJobGraphConnected() (toil.job.Job method)
checkJobGraphForDeadlocks() (toil.job.Job method)
checkNewCheckpointsAreLeafVertices() (toil.job.Job method)
clean() (toil.jobStores.abstractJobStore.AbstractJobStore method)
ConcurrentFileModificationException
config (toil.common.Toil attribute)
(toil.jobStores.abstractJobStore.AbstractJobStore attribute)
convertPromises() (toil.job.PromisedRequirement static method)
create() (toil.jobStores.abstractJobStore.AbstractJobStore method)
createBatchSystem() (toil.common.Toil static method)
createRootJob() (toil.jobStores.abstractJobStore.AbstractJobStore method)
D
defer() (toil.job.Job method)
delete() (toil.jobStores.abstractJobStore.AbstractJobStore method)
deleteFile() (toil.jobStores.abstractJobStore.AbstractJobStore method)
deleteGlobalFile() (toil.fileStore.FileStore method)
deleteLocalFile() (toil.fileStore.FileStore method)
destroy() (toil.jobStores.abstractJobStore.AbstractJobStore method)
E
encapsulate() (toil.job.Job method)
EncapsulatedJob (class in toil.job)
exists() (toil.jobStores.abstractJobStore.AbstractJobStore method)
exportFile() (toil.common.Toil method)
(toil.jobStores.abstractJobStore.AbstractJobStore method)
F
fileExists() (toil.jobStores.abstractJobStore.AbstractJobStore method)
filesToDelete (toil.job.Promise attribute)
FileStore (class in toil.fileStore)
findAndHandleDeadJobs() (toil.fileStore.FileStore class method)
FunctionWrappingJob (class in toil.job)
G
getDefaultArgumentParser() (toil.job.Job.Runner static method)
getDefaultOptions() (toil.job.Job.Runner static method)
getEmptyFileStoreID() (toil.jobStores.abstractJobStore.AbstractJobStore method)
getEnv() (toil.jobStores.abstractJobStore.AbstractJobStore method)
getIssuedBatchJobIDs() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
getJobStore() (toil.common.Toil class method)
getLocalTempDir() (toil.fileStore.FileStore method)
getLocalTempFile() (toil.fileStore.FileStore method)
getLocalTempFileName() (toil.fileStore.FileStore method)
getPublicUrl() (toil.jobStores.abstractJobStore.AbstractJobStore method)
getRescueBatchJobFrequency() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem class method)
getRootJobs() (toil.job.Job method)
getRunningBatchJobIDs() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
getSharedPublicUrl() (toil.jobStores.abstractJobStore.AbstractJobStore method)
getSize() (toil.jobStores.abstractJobStore.AbstractJobStore class method)
getTopologicalOrderingOfJobs() (toil.job.Job method)
getUpdatedBatchJob() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
getValue() (toil.job.PromisedRequirement method)
getWorkflowDir() (toil.common.Toil static method)
H
hasChild() (toil.job.Job method)
I
importFile() (toil.common.Toil method)
(toil.jobStores.abstractJobStore.AbstractJobStore method)
initialize() (toil.jobStores.abstractJobStore.AbstractJobStore method)
issueBatchJob() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
J
Job (class in toil.job)
Job.Runner (class in toil.job)
Job.Service (class in toil.job)
JobException
JobFunctionWrappingJob (class in toil.job)
JobGraphDeadlockException
jobs() (toil.jobStores.abstractJobStore.AbstractJobStore method)
JobStoreExistsException
K
killBatchJobs() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
L
load() (toil.jobStores.abstractJobStore.AbstractJobStore method)
loadRootJob() (toil.jobStores.abstractJobStore.AbstractJobStore method)
logToMaster() (toil.fileStore.FileStore method)
N
NoSuchFileException
NoSuchJobException
NoSuchJobStoreException
O
open() (toil.fileStore.FileStore method)
P
prepareForPromiseRegistration() (toil.job.Job method)
Promise (class in toil.job)
PromisedRequirement (class in toil.job)
R
readFile() (toil.jobStores.abstractJobStore.AbstractJobStore method)
readFileStream() (toil.jobStores.abstractJobStore.AbstractJobStore method)
readGlobalFile() (toil.fileStore.FileStore method)
readGlobalFileStream() (toil.fileStore.FileStore method)
readSharedFileStream() (toil.jobStores.abstractJobStore.AbstractJobStore method)
readStatsAndLogging() (toil.jobStores.abstractJobStore.AbstractJobStore method)
restart() (toil.common.Toil method)
resume() (toil.jobStores.abstractJobStore.AbstractJobStore method)
run() (toil.job.Job method)
rv() (toil.job.Job method)
S
setEnv() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
setOptions() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem class method)
setRootJob() (toil.jobStores.abstractJobStore.AbstractJobStore method)
setUserScript() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
shutdown() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
(toil.fileStore.FileStore class method)
start() (toil.common.Toil method)
(toil.job.Job.Service method)
startToil() (toil.job.Job.Runner static method)
stop() (toil.job.Job.Service method)
supportsHotDeployment() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem class method)
supportsWorkerCleanup() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem class method)
T
Toil (class in toil.common)
U
update() (toil.jobStores.abstractJobStore.AbstractJobStore method)
updateFile() (toil.jobStores.abstractJobStore.AbstractJobStore method)
updateFileStream() (toil.jobStores.abstractJobStore.AbstractJobStore method)
W
wrapFn() (toil.job.Job static method)
wrapJobFn() (toil.job.Job static method)
writeConfig() (toil.jobStores.abstractJobStore.AbstractJobStore method)
writeFile() (toil.jobStores.abstractJobStore.AbstractJobStore method)
writeFileStream() (toil.jobStores.abstractJobStore.AbstractJobStore method)
writeGlobalFile() (toil.fileStore.FileStore method)
writeGlobalFileStream() (toil.fileStore.FileStore method)
writeSharedFileStream() (toil.jobStores.abstractJobStore.AbstractJobStore method)
writeStatsAndLogging() (toil.jobStores.abstractJobStore.AbstractJobStore method)
Table Of Contents
Getting Started
Overview
Installation
Quickstart Examples
Running Toil
Overview
Toil Workflow Options and Command Line Interface
CWL in Toil
Deploying a Workflow
Running in AWS
Running in Azure
Running in Openstack
Running in GCE
Running in HPC Environments
Developing Toil Workflows
Overview
Developing a Workflow
Toil API
Batch System API
Job Store API
Contributing to Toil
Overview
Running tests
Developing with the Toil Appliance
Maintainer’s Guidelines
Appendices
Toil Architecture
Toil Environment Variables
Related Topics
Documentation overview
Quick search