Index

_ | A | C | D | E | F | G | H | I | J | K | L | 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)

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)
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.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)
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.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 (class in toil.job)
JobFunctionWrappingJob (class in toil.job)
JobGraphDeadlockException (class in toil.job)
jobs() (toil.jobStores.abstractJobStore.AbstractJobStore method)

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)

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)
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)