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galaxy.jobs.runners.util.cli.job package¶
Abstract base class for cli job plugins.
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class
galaxy.jobs.runners.util.cli.job.
BaseJobExec
(**params)[source]¶ Bases:
object
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job_script_kwargs
(ofile, efile, job_name)[source]¶ Return extra keyword argument for consumption by job script module.
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abstract
submit
(script_file)[source]¶ Given specified script_file path, yield command to submit it to external job manager.
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abstract
delete
(job_id)[source]¶ Given job id, return command to stop execution or dequeue specified job.
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abstract
get_single_status
(job_id)[source]¶ Return command to get the status of a single, specified job.
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abstract
parse_status
(status, job_ids)[source]¶ Parse the statuses of output from get_status command.
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galaxy.jobs.runners.util.cli.job.
job_states
¶ alias of
galaxy.model.Job.states
Submodules¶
galaxy.jobs.runners.util.cli.job.lsf module¶
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class
galaxy.jobs.runners.util.cli.job.lsf.
LSF
(**params)[source]¶ Bases:
galaxy.jobs.runners.util.cli.job.BaseJobExec
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job_script_kwargs
(ofile, efile, job_name)[source]¶ Return extra keyword argument for consumption by job script module.
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submit
(script_file)[source]¶ Given specified script_file path, yield command to submit it to external job manager.
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galaxy.jobs.runners.util.cli.job.slurm module¶
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class
galaxy.jobs.runners.util.cli.job.slurm.
Slurm
(**params)[source]¶ Bases:
galaxy.jobs.runners.util.cli.job.BaseJobExec
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job_script_kwargs
(ofile, efile, job_name)[source]¶ Return extra keyword argument for consumption by job script module.
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galaxy.jobs.runners.util.cli.job.slurm_torque module¶
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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.
galaxy.jobs.runners.util.cli.job.torque module¶
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class
galaxy.jobs.runners.util.cli.job.torque.
Torque
(**params)[source]¶ Bases:
galaxy.jobs.runners.util.cli.job.BaseJobExec
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job_script_kwargs
(ofile, efile, job_name)[source]¶ Return extra keyword argument for consumption by job script module.
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