Toil Class API¶
The Toil class configures and starts a Toil run.
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class
toil.common.
Toil
(options)[source]¶ A context manager that represents a Toil workflow, specifically the batch system, job store, and its configuration.
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__init__
(options)[source]¶ Initialize a Toil object from the given options. Note that this is very light-weight and that the bulk of the work is done when the context is entered.
Parameters: options (argparse.Namespace) – command line options specified by the user
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config
= None¶ Type: toil.common.Config
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start
(rootJob)[source]¶ Invoke a Toil workflow with the given job as the root for an initial run. This method must be called in the body of a
with Toil(...) as toil:
statement. This method should not be called more than once for a workflow that has not finished.Parameters: rootJob (toil.job.Job) – The root job of the workflow Returns: The root job’s return value
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restart
()[source]¶ Restarts a workflow that has been interrupted.
Returns: The root job’s return value
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classmethod
getJobStore
(locator)[source]¶ Create an instance of the concrete job store implementation that matches the given locator.
Parameters: locator (str) – The location of the job store to be represent by the instance Returns: an instance of a concrete subclass of AbstractJobStore Return type: toil.jobStores.abstractJobStore.AbstractJobStore
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static
createBatchSystem
(config)[source]¶ Creates an instance of the batch system specified in the given config.
Parameters: config (toil.common.Config) – the current configuration Return type: batchSystems.abstractBatchSystem.AbstractBatchSystem Returns: an instance of a concrete subclass of AbstractBatchSystem
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importFile
(srcUrl, sharedFileName=None)[source]¶ Imports the file at the given URL into job store.
See
toil.jobStores.abstractJobStore.AbstractJobStore.importFile()
for a full description
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exportFile
(jobStoreFileID, dstUrl)[source]¶ Exports file to destination pointed at by the destination URL.
See
toil.jobStores.abstractJobStore.AbstractJobStore.exportFile()
for a full description
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static
getToilWorkDir
(configWorkDir=None)[source]¶ Returns a path to a writable directory under which per-workflow directories exist. This directory is always required to exist on a machine, even if the Toil worker has not run yet. If your workers and leader have different temp directories, you may need to set TOIL_WORKDIR.
Parameters: configWorkDir (str) – Value passed to the program using the –workDir flag Returns: Path to the Toil work directory, constant across all machines Return type: str
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