toil.batchSystems.local_support

Attributes

logger

Classes

BatchSystemLocalSupport

Adds a local queue for helper jobs, useful for CWL & others.

Module Contents

toil.batchSystems.local_support.logger

class toil.batchSystems.local_support.BatchSystemLocalSupport(config, maxCores, maxMemory, maxDisk)

Bases: toil.batchSystems.abstractBatchSystem.BatchSystemSupport

Adds a local queue for helper jobs, useful for CWL & others.

Parameters:

• config (toil.common.Config)

• maxCores (float)

• maxMemory (int)

• maxDisk (int)

max_local_jobs

localBatch: toil.batchSystems.singleMachine.SingleMachineBatchSystem

handleLocalJob(command, jobDesc)

To be called by issueBatchJob.

Returns the jobID if the jobDesc has been submitted to the local queue, otherwise returns None

Parameters:

• command (str)

• jobDesc (toil.job.JobDescription)

Return type:

Optional[int]

killLocalJobs(jobIDs)

Will kill all local jobs that match the provided jobIDs.

To be called by killBatchJobs.

Parameters:

jobIDs (List[int])

Return type:

None

getIssuedLocalJobIDs()

To be called by getIssuedBatchJobIDs.

Return type:

List[int]

getRunningLocalJobIDs()

To be called by getRunningBatchJobIDs().

Return type:

Dict[int, float]

getUpdatedLocalJob(maxWait)

To be called by getUpdatedBatchJob().

Parameters:

maxWait (int)

Return type:

Optional[toil.batchSystems.abstractBatchSystem.UpdatedBatchJobInfo]

getNextJobID()

Must be used to get job IDs so that the local and batch jobs do not conflict.

Return type:

int

shutdownLocal()

To be called from shutdown().

Return type:

None