Index
_
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A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
W
_
__init__() (toil.common.Toil method)
(toil.fileStores.FileID method)
(toil.fileStores.abstractFileStore.AbstractFileStore 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)
AbstractFileStore (class in toil.fileStores.abstractFileStore)
AbstractJobStore (class in toil.jobStores.abstractJobStore)
addChild() (toil.job.EncapsulatedJob method)
(toil.job.Job method)
addChildFn() (toil.job.Job method)
addChildJobFn() (toil.job.Job method)
addFollowOn() (toil.job.EncapsulatedJob method)
(toil.job.Job method)
addFollowOnFn() (toil.job.Job method)
addFollowOnJobFn() (toil.job.Job method)
addService() (toil.job.EncapsulatedJob method)
(toil.job.Job method)
addToilOptions() (toil.job.Job.Runner static method)
B
batch() (toil.jobStores.abstractJobStore.AbstractJobStore 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.fileStores.abstractFileStore.AbstractFileStore method)
deleteLocalFile() (toil.fileStores.abstractFileStore.AbstractFileStore 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)
FileID (class in toil.fileStores)
filesToDelete (toil.job.Promise attribute)
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)
getFileSize() (toil.jobStores.abstractJobStore.AbstractJobStore method)
getGlobalFileSize() (toil.fileStores.abstractFileStore.AbstractFileStore method)
getIssuedBatchJobIDs() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
getJobStore() (toil.common.Toil class 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)
getPublicUrl() (toil.jobStores.abstractJobStore.AbstractJobStore method)
getRootJobReturnValue() (toil.jobStores.abstractJobStore.AbstractJobStore 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)
getToilWorkDir() (toil.common.Toil static method)
getTopologicalOrderingOfJobs() (toil.job.Job method)
getUpdatedBatchJob() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
getValue() (toil.job.PromisedRequirement method)
H
hasChild() (toil.job.Job method)
hasFollowOn() (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)
log() (toil.job.Job method)
logToMaster() (toil.fileStores.abstractFileStore.AbstractFileStore method)
N
NoSuchFileException
NoSuchJobException
NoSuchJobStoreException
O
open() (toil.fileStores.abstractFileStore.AbstractFileStore method)
P
pack() (toil.fileStores.FileID method)
prepareForPromiseRegistration() (toil.job.EncapsulatedJob method)
(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.fileStores.abstractFileStore.AbstractFileStore method)
readGlobalFileStream() (toil.fileStores.abstractFileStore.AbstractFileStore 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.FunctionWrappingJob method)
(toil.job.Job method)
(toil.job.JobFunctionWrappingJob method)
rv() (toil.job.EncapsulatedJob method)
(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.fileStores.abstractFileStore.AbstractFileStore class method)
shutdownFileStore() (toil.fileStores.abstractFileStore.AbstractFileStore static method)
start() (toil.common.Toil method)
(toil.job.Job.Service method)
startCommit() (toil.fileStores.abstractFileStore.AbstractFileStore method)
startToil() (toil.job.Job.Runner static method)
stop() (toil.job.Job.Service method)
supportsAutoDeployment() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem class method)
supportsWorkerCleanup() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem class method)
T
tempDir (toil.job.Job attribute)
Toil (class in toil.common)
U
unpack() (toil.fileStores.FileID class method)
update() (toil.jobStores.abstractJobStore.AbstractJobStore method)
updateFile() (toil.jobStores.abstractJobStore.AbstractJobStore method)
updateFileStream() (toil.jobStores.abstractJobStore.AbstractJobStore method)
W
waitForCommit() (toil.fileStores.abstractFileStore.AbstractFileStore method)
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.fileStores.abstractFileStore.AbstractFileStore method)
writeGlobalFileStream() (toil.fileStores.abstractFileStore.AbstractFileStore method)
writePIDFile() (toil.common.Toil method)
writeSharedFileStream() (toil.jobStores.abstractJobStore.AbstractJobStore method)
writeStatsAndLogging() (toil.jobStores.abstractJobStore.AbstractJobStore method)
Toil
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