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galaxy.jobs.runners.util.cli package

class galaxy.jobs.runners.util.cli.CliInterface

Bases: object

High-level interface for loading shell and job plugins and matching them to specified parameters.

__init__()

get_plugins(shell_params, job_params)

Return shell and job interface defined by and configured via specified params.

get_shell_plugin(shell_params)

get_job_interface(job_params)

galaxy.jobs.runners.util.cli.split_params(params)

Subpackages

• galaxy.jobs.runners.util.cli.job package
  • BaseJobExec
    • BaseJobExec.__init__()
    • BaseJobExec.job_script_kwargs()
    • BaseJobExec.submit()
    • BaseJobExec.delete()
    • BaseJobExec.get_status()
    • BaseJobExec.get_single_status()
    • BaseJobExec.parse_status()
    • BaseJobExec.parse_single_status()
    • BaseJobExec.get_failure_reason()
    • BaseJobExec.parse_failure_reason()
  • job_states
  • Submodules
  • galaxy.jobs.runners.util.cli.job.lsf module
    • LSF
      • LSF.job_script_kwargs()
      • LSF.submit()
      • LSF.delete()
      • LSF.get_status()
      • LSF.get_single_status()
      • LSF.parse_status()
      • LSF.parse_single_status()
      • LSF.get_failure_reason()
      • LSF.parse_failure_reason()
  • galaxy.jobs.runners.util.cli.job.pbs module
    • OpenPBS
      • OpenPBS.ERROR_MESSAGE_UNRECOGNIZED_ARG
      • OpenPBS.get_status()
      • OpenPBS.get_single_status()
      • OpenPBS.parse_status()
  • galaxy.jobs.runners.util.cli.job.slurm module
    • Slurm
      • Slurm.job_script_kwargs()
      • Slurm.submit()
      • Slurm.delete()
      • Slurm.get_status()
      • Slurm.get_single_status()
      • Slurm.parse_status()
      • Slurm.parse_single_status()
  • galaxy.jobs.runners.util.cli.job.slurm_torque module
    • SlurmTorque
      • SlurmTorque.get_status()
      • SlurmTorque.parse_status()
  • galaxy.jobs.runners.util.cli.job.torque module
    • Torque
      • Torque.ERROR_MESSAGE_UNRECOGNIZED_ARG
      • Torque.job_script_kwargs()
      • Torque.submit()
      • Torque.delete()
      • Torque.get_status()
      • Torque.get_single_status()
      • Torque.parse_status()
      • Torque.parse_single_status()
• galaxy.jobs.runners.util.cli.shell package
  • BaseShellExec
    • BaseShellExec.__init__()
    • BaseShellExec.execute()
  • Submodules
  • galaxy.jobs.runners.util.cli.shell.local module
    • LocalShell
      • LocalShell.__init__()
      • LocalShell.execute()
  • galaxy.jobs.runners.util.cli.shell.rsh module
    • RemoteShell
      • RemoteShell.__init__()
      • RemoteShell.execute()
    • SecureShell
      • SecureShell.__init__()
    • GlobusSecureShell
      • GlobusSecureShell.__init__()
    • ParamikoShell
      • ParamikoShell.__init__()
      • ParamikoShell.connect()
      • ParamikoShell.execute()

Submodules

galaxy.jobs.runners.util.cli.factory module

galaxy.jobs.runners.util.cli.factory.build_cli_interface()

galaxy.jobs.runners.util.cli.factory.get_shell(params)