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CLI

Bioluigi provides a command-line interface tool to interact more conveniently with Luigi scheduler.

List and filter tasks

List all the tasks that match the given filters.

bioluigi list [--status] [--detailed] [--no-limit] [TASK_GLOB]
  • --status is used to filter tasks by status (i.e. PENDING, RUNNING, DONE, ...) and can be specified multiple times.
  • --detailed triggers the detailed view produced by bioluigi view subcommand.
  • --no-limit disable the limit to the number of returned tasks by the scheduler. Note that this might freeze the scheduler thread for a couple of seconds if a large number of tasks is queried.
  • TASK_GLOB is a UNIX glob pattern that match tasks names and identifiers according to :pyfnmatch.fnmatch rules.

View a task

Given a task identifier, this subcommand will display the details of a task.

bioluigi show TASK_ID
  • TASK_ID is a task identifier.

Forgive a failed task

Forgive a failed task which will update its status to PENDING.

bioluigi forgive [--recursive] TASK_ID
  • TASK_ID is a task identifier.
  • --recursive recursively forgive the task dependencies

Re-enable a disabled task

Re-enable a disabled task which will update its status to FAILED.

bioluigi reenable [--recursive] TASK_ID
  • TASK_ID is a task identifier.
  • --recursive recursively re-enable the task dependencies