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(jobstore_as_flag=False)[source]

Get argument parser with added toil workflow options.

This is the Right Way to get an argument parser in a Toil Python workflow.

Parameters:

jobstore_as_flag (bool) – make the job store option a –jobStore flag instead of a required jobStore positional argument.

Return type:

ArgumentParser

Returns:

The argument parser used by a toil workflow with added Toil options.

static getDefaultOptions(jobStore=None, jobstore_as_flag=False)[source]

Get default options for a toil workflow.

Parameters:

  • jobStore (str | PathLike[str] | None) – A string describing the jobStore for the workflow.

  • jobstore_as_flag (bool) – make the job store option a –jobStore flag instead of a required jobStore positional argument.

Return type:

Namespace

Returns:

The options used by a toil workflow.

static addToilOptions(parser, jobstore_as_flag=False)[source]

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

Consider using getDefaultArgumentParser() instead, which will produce a parser of the correct class to use Toil’s config file and environment variables. If ther parser passed here is just an argparse.ArgumentParser and not a configargparse.ArgParser, the Toil config file and environment variables will not be respected.

Parameters:

  • parser (OptionParser | ArgumentParser) – Options object to add toil options to.

  • jobstore_as_flag (bool) – make the job store option a –jobStore flag instead of a required jobStore positional argument.

Return type:

None

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. :type job: Job :param job: root job of the workflow :raises: toil.exceptions.FailedJobsException if at the end of function there remain failed jobs. :rtype: Any :return: The return value of the root job’s run function.

Parameters:
Return type:

Any