Job.Runner API¶
The Runner contains the methods needed to configure and start a Toil run.
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class
Job.
Runner
[source]¶ Used to setup and run Toil workflow.
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static
getDefaultArgumentParser
() → argparse.ArgumentParser[source]¶ Get argument parser with added toil workflow options.
Returns: The argument parser used by a toil workflow with added Toil options. Return type: argparse.ArgumentParser
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static
getDefaultOptions
(jobStore: str) → argparse.Namespace[source]¶ Get default options for a toil workflow.
Parameters: jobStore (string) – A string describing the jobStore for the workflow. Returns: The options used by a toil workflow. Return type: argparse.ArgumentParser values object
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static
addToilOptions
(parser)[source]¶ Adds the default toil options to an
optparse
orargparse
parser object.Parameters: parser (optparse.OptionParser or argparse.ArgumentParser) – Options object to add toil options to.
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static
startToil
(job, options)[source]¶ Run the toil workflow using the given options.
Deprecated by toil.common.Toil.start.
(see Job.Runner.getDefaultOptions and Job.Runner.addToilOptions) starting with this job. :param toil.job.Job job: root job of the workflow :raises: toil.leader.FailedJobsException if at the end of function their remain failed jobs. :return: The return value of the root job’s run function. :rtype: Any
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static