Warning

This document is for an old release 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.

abstract submit(script_file)[source]

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

abstract delete(job_id)[source]

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

abstract get_status(job_ids=None)[source]

Return command to get statuses of specified job ids.

abstract get_single_status(job_id)[source]

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

abstract parse_status(status, job_ids)[source]

Parse the statuses of output from get_status command.

abstract parse_single_status(status, job_id)[source]

Parse the status of output from get_single_status command.

get_failure_reason(job_id)[source]

Return the failure reason for the given job_id.

parse_failure_reason(reason, job_id)[source]

Parses the failure reason, assigning it against a

galaxy.jobs.runners.util.cli.job.job_states

alias of galaxy.model.Job.states

Submodules

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

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

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

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.

get_failure_reason(job_id)[source]

Return the failure reason for the given job_id.

parse_failure_reason(reason, job_id)[source]

Parses the failure reason, assigning it against a

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

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

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

ERROR_MESSAGE_UNRECOGNIZED_ARG = 'Unrecognized long argument passed to OpenPBS CLI plugin: %s'
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.

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

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.

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]

Return command to get statuses of specified job ids.

parse_status(status, job_ids)[source]

Parse the statuses of output from get_status command.

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

ERROR_MESSAGE_UNRECOGNIZED_ARG = 'Unrecognized long argument passed to Torque CLI plugin: %s'
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.