Job.Runner API

The Runner contains the methods needed to configure and start a Toil run.

class Job.Runner[source]

Used to setup and run Toil workflow.

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
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
static addToilOptions(parser)[source]

Adds the default toil options to an optparse or argparse parser object.

Parameters:parser (optparse.OptionParser or argparse.ArgumentParser) – Options object to add toil options to.
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