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
- 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_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.
Submodules¶
galaxy.jobs.runners.util.cli.job.lsf module¶
- class galaxy.jobs.runners.util.cli.job.lsf.LSF(**params)[source]¶
Bases:
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.
galaxy.jobs.runners.util.cli.job.pbs module¶
galaxy.jobs.runners.util.cli.job.slurm module¶
- class galaxy.jobs.runners.util.cli.job.slurm.Slurm(**params)[source]¶
Bases:
BaseJobExec
- job_script_kwargs(ofile, efile, job_name)[source]¶
Return extra keyword argument for consumption by job script module.
galaxy.jobs.runners.util.cli.job.slurm_torque module¶
galaxy.jobs.runners.util.cli.job.torque module¶
- class galaxy.jobs.runners.util.cli.job.torque.Torque(**params)[source]¶
Bases:
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.