Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
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.JobDescription 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)
add_options() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem class method)
addChild() (toil.job.EncapsulatedJob method)
(toil.job.Job method)
(toil.job.JobDescription method)
addChildFn() (toil.job.Job method)
addChildJobFn() (toil.job.Job method)
addFollowOn() (toil.job.EncapsulatedJob method)
(toil.job.Job method)
(toil.job.JobDescription method)
addFollowOnFn() (toil.job.Job method)
addFollowOnJobFn() (toil.job.Job method)
addPredecessor() (toil.job.JobDescription method)
addService() (toil.job.EncapsulatedJob method)
(toil.job.Job method)
addServiceHostJob() (toil.job.JobDescription method)
addToilOptions() (toil.job.Job.Runner static method)
allSuccessors() (toil.job.JobDescription method)
assign_job_id() (toil.jobStores.abstractJobStore.AbstractJobStore method)
assignConfig() (toil.job.Job 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)
checkpoint (toil.job.Job attribute)
clean() (toil.jobStores.abstractJobStore.AbstractJobStore method)
clearRemainingTryCount() (toil.job.JobDescription method)
clearSuccessorsAndServiceHosts() (toil.job.JobDescription method)
ConcurrentFileModificationException
config (toil.jobStores.abstractJobStore.AbstractJobStore attribute)
convertPromises() (toil.job.PromisedRequirement static method)
cores (toil.job.Job attribute)
create_job() (toil.jobStores.abstractJobStore.AbstractJobStore method)
create_root_job() (toil.jobStores.abstractJobStore.AbstractJobStore method)
createBatchSystem() (toil.common.Toil static method)
createFileStore() (toil.fileStores.abstractFileStore.AbstractFileStore static method)
D
defer() (toil.job.Job method)
delete_file() (toil.jobStores.abstractJobStore.AbstractJobStore method)
delete_job() (toil.jobStores.abstractJobStore.AbstractJobStore method)
deleteGlobalFile() (toil.fileStores.abstractFileStore.AbstractFileStore method)
deleteLocalFile() (toil.fileStores.abstractFileStore.AbstractFileStore method)
description (toil.job.Job attribute)
destroy() (toil.jobStores.abstractJobStore.AbstractJobStore method)
disk (toil.job.Job attribute)
E
encapsulate() (toil.job.Job method)
EncapsulatedJob (class in toil.job)
export_file() (toil.common.Toil method)
(toil.jobStores.abstractJobStore.AbstractJobStore method)
F
file_exists() (toil.jobStores.abstractJobStore.AbstractJobStore method)
fileExists() (toil.jobStores.abstractJobStore.AbstractJobStore method)
FileID (class in toil.fileStores)
filesToDelete (toil.job.Promise attribute)
filterServiceHosts() (toil.job.JobDescription method)
filterSuccessors() (toil.job.JobDescription method)
FunctionWrappingJob (class in toil.job)
G
get_empty_file_store_id() (toil.jobStores.abstractJobStore.AbstractJobStore method)
get_env() (toil.jobStores.abstractJobStore.AbstractJobStore method)
get_file_size() (toil.jobStores.abstractJobStore.AbstractJobStore method)
get_is_directory() (toil.jobStores.abstractJobStore.AbstractJobStore class method)
get_local_workflow_coordination_dir() (toil.common.Toil class method)
get_public_url() (toil.jobStores.abstractJobStore.AbstractJobStore method)
get_root_job_return_value() (toil.jobStores.abstractJobStore.AbstractJobStore method)
get_shared_public_url() (toil.jobStores.abstractJobStore.AbstractJobStore method)
get_size() (toil.jobStores.abstractJobStore.AbstractJobStore class method)
get_toil_coordination_dir() (toil.common.Toil class method)
getDefaultArgumentParser() (toil.job.Job.Runner static method)
getDefaultOptions() (toil.job.Job.Runner static 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)
getLogFileHandle() (toil.job.JobDescription method)
getRootJobs() (toil.job.Job method)
getRunningBatchJobIDs() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
getSchedulingStatusMessage() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
getToilWorkDir() (toil.common.Toil static method)
getTopologicalOrderingOfJobs() (toil.job.Job method)
getUpdatedBatchJob() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
getValue() (toil.job.PromisedRequirement method)
getWorkerContexts() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
H
hasChild() (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)
I
import_file() (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)
job_exists() (toil.jobStores.abstractJobStore.AbstractJobStore method)
JobDescription (class in toil.job)
JobException
JobFunctionWrappingJob (class in toil.job)
JobGraphDeadlockException
jobs() (toil.jobStores.abstractJobStore.AbstractJobStore method)
JobStoreExistsException
jobStoreID (toil.job.Job attribute)
K
killBatchJobs() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
L
list_url() (toil.jobStores.abstractJobStore.AbstractJobStore class method)
load_job() (toil.jobStores.abstractJobStore.AbstractJobStore method)
load_root_job() (toil.jobStores.abstractJobStore.AbstractJobStore method)
loadJob() (toil.job.Job class method)
locator (toil.jobStores.abstractJobStore.AbstractJobStore attribute)
log() (toil.job.Job method)
logAccess() (toil.fileStores.abstractFileStore.AbstractFileStore method)
logToMaster() (toil.fileStores.abstractFileStore.AbstractFileStore method)
M
memory (toil.job.Job attribute)
N
nextSuccessors() (toil.job.JobDescription method)
normalize_uri() (toil.common.Toil static method)
NoSuchFileException
NoSuchJobException
NoSuchJobStoreException
O
onRegistration() (toil.job.JobDescription method)
open() (toil.fileStores.abstractFileStore.AbstractFileStore method)
P
pack() (toil.fileStores.FileID method)
pre_update_hook() (toil.job.JobDescription method)
preemptable (toil.job.Job attribute)
prepareForPromiseRegistration() (toil.job.EncapsulatedJob method)
(toil.job.Job method)
Promise (class in toil.job)
PromisedRequirement (class in toil.job)
R
read_file() (toil.jobStores.abstractJobStore.AbstractJobStore method)
read_file_stream() (toil.jobStores.abstractJobStore.AbstractJobStore method)
read_from_url() (toil.jobStores.abstractJobStore.AbstractJobStore class method)
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_logs() (toil.jobStores.abstractJobStore.AbstractJobStore method)
read_shared_file_stream() (toil.jobStores.abstractJobStore.AbstractJobStore method)
readGlobalFile() (toil.fileStores.abstractFileStore.AbstractFileStore method)
readGlobalFileStream() (toil.fileStores.abstractFileStore.AbstractFileStore method)
remainingTryCount (toil.job.JobDescription attribute)
renameReferences() (toil.job.JobDescription method)
replace() (toil.job.JobDescription 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
saveAsRootJob() (toil.job.Job method)
saveBody() (toil.job.Job method)
serviceHostIDsInBatches() (toil.job.JobDescription method)
services (toil.job.JobDescription attribute)
set_root_job() (toil.jobStores.abstractJobStore.AbstractJobStore method)
setEnv() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem method)
setOptions() (toil.batchSystems.abstractBatchSystem.AbstractBatchSystem class method)
setRootJob() (toil.jobStores.abstractJobStore.AbstractJobStore method)
setupJobAfterFailure() (toil.job.JobDescription 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)
stack (toil.job.JobDescription attribute)
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)
successorsAndServiceHosts() (toil.job.JobDescription 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_file() (toil.jobStores.abstractJobStore.AbstractJobStore method)
update_file_stream() (toil.jobStores.abstractJobStore.AbstractJobStore method)
update_job() (toil.jobStores.abstractJobStore.AbstractJobStore method)
updateFile() (toil.jobStores.abstractJobStore.AbstractJobStore method)
W
waitForCommit() (toil.fileStores.abstractFileStore.AbstractFileStore method)
wrapFn() (toil.job.Job static method)
wrapJobFn() (toil.job.Job static method)
write_config() (toil.jobStores.abstractJobStore.AbstractJobStore method)
write_file() (toil.jobStores.abstractJobStore.AbstractJobStore method)
write_file_stream() (toil.jobStores.abstractJobStore.AbstractJobStore method)
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_logs() (toil.jobStores.abstractJobStore.AbstractJobStore method)
write_shared_file_stream() (toil.jobStores.abstractJobStore.AbstractJobStore method)
writeGlobalFile() (toil.fileStores.abstractFileStore.AbstractFileStore method)
writeGlobalFileStream() (toil.fileStores.abstractFileStore.AbstractFileStore method)
Toil
Navigation
Getting Started
Installation
Quickstart Examples
Running Toil
Introduction
Commandline Options
Toil Debugging
Running in the Cloud
Cloud Platforms
HPC Environments
CWL in Toil
WDL in Toil
Workflow Execution Service (WES)
Developing Toil Workflows
Developing a Workflow
Toil Class API
Job Store API
Toil Job API
Job Methods API
Job.Runner API
job.fileStore API
Batch System API
Job.Service API
Exceptions API
Contributing to Toil
Running Tests
Developing with Docker
Maintainer’s Guidelines
Pull Request Checklists
Appendices
Toil Architecture
Minimum AWS IAM permissions
Auto-Deployment
Environment Variables
Related Topics
Documentation overview
Quick search