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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.

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

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

__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.

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.slurm module

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

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

__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.

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

__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.