Warning

This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

galaxy.jobs.runners.util.cli.job package

Abstract base class for cli job plugins.

class galaxy.jobs.runners.util.cli.job.BaseJobExec(**params)[source]

Bases: object

__init__(**params)[source]

Constructor for CLI job executor.

job_script_kwargs(ofile, efile, job_name)[source]

Return extra keyword argument for consumption by job script module.

submit(script_file)[source]

Given specified script_file path, yield command to submit it to external job manager.

delete(job_id)[source]

Given job id, return command to stop execution or dequeue specified job.

get_status(job_ids=None)[source]

Return command to get statuses of specified job ids.

get_single_status(job_id)[source]

Return command to get the status of a single, specified job.

parse_status(status, job_ids)[source]

Parse the statuses of output from get_status command.

parse_single_status(status, job_id)[source]

Parse the status of output from get_single_status command.

Submodules

galaxy.jobs.runners.util.cli.job.slurm module

class galaxy.jobs.runners.util.cli.job.slurm.Slurm(**params)[source]

Bases: galaxy.jobs.runners.util.cli.job.BaseJobExec

__init__(**params)[source]
job_script_kwargs(ofile, efile, job_name)[source]
submit(script_file)[source]
delete(job_id)[source]
get_status(job_ids=None)[source]
get_single_status(job_id)[source]
parse_status(status, job_ids)[source]
parse_single_status(status, job_id)[source]

galaxy.jobs.runners.util.cli.job.slurm_torque module

class galaxy.jobs.runners.util.cli.job.slurm_torque.SlurmTorque(**params)[source]

Bases: galaxy.jobs.runners.util.cli.job.torque.Torque

A CLI job executor for Slurm’s Torque compatibility mode. This differs from real torque CLI in that -x command line is not available so job status needs to be parsed from qstat table instead of XML.

get_status(job_ids=None)[source]
parse_status(status, job_ids)[source]

galaxy.jobs.runners.util.cli.job.torque module

class galaxy.jobs.runners.util.cli.job.torque.Torque(**params)[source]

Bases: galaxy.jobs.runners.util.cli.job.BaseJobExec

__init__(**params)[source]
job_script_kwargs(ofile, efile, job_name)[source]
submit(script_file)[source]
delete(job_id)[source]
get_status(job_ids=None)[source]
get_single_status(job_id)[source]
parse_status(status, job_ids)[source]
parse_single_status(status, job_id)[source]