Command Line Interface

BEE is controlled by one “beeflow” command with sub-commands to do various operations with the client or daemon.

BEE Daemon

To interact with the daemon process you’ll need to use the beeflow core sub-command. The following are the options:

beeflow core start: Daemonize (if not in debug) and start all BEE components.

Options:
-F, --foreground

run in the foreground [default: False]

beeflow core status: Check the status of beeflow and the components.

beeflow core stop: Stop the current running beeflow daemon.

beeflow core --version: Display the version number of BEE.

Submission and workflow commands

This section shows what commands you can use to submit and interact with your workflows. The following are the major options:

beeflow submit: Submit a new workflow. By default this will also start jobs immediately (unless passed the --no-start option). If either the MAIN_CWL or YAML files are not contained immediately inside of WF_PATH, then the WF_PATH directory will be copied into a temporary directory and the missing files will then be copied into the copied WF_PATH directory before packaging and submission.

Arguments:

  • WF_NAME, The workflow name [required]

  • WF_PATH, Path to the workflow CWL tarball or directory [required]

  • MAIN_CWL, filename of main CWL file [required]

  • YAML, filename of YAML file [required]

  • WORKDIR, working directory for workflow containing input + output files [required]

  • --no-start, don’t start the workflow immediately

beeflow start: Start a workflow with a workflow ID. Only needed if beeflow submit was passed the --no-start option.

Arguments:

  • WF_ID [required]

beeflow package: Package a workflow into a tarball.

Arguments:

  • WF_PATH, Path to the workflow package directory [required]

  • PACKAGE_DEST, Path for where the packaged workflow should be saved [required]

beeflow list: List all workflows

beeflow query: Get the status of a workflow.

Arguments:

  • WF_ID [required]

beeflow pause: Pause a workflow (Running tasks will finish)

Arguments:

WF_ID [required]

beeflow resume: Resume a paused workflow.

Arguments:

WF_ID [required]

beeflow cancel: Cancel a workflow.

Arguments:

WF_ID [required]

beeflow copy: Copy an archived workflow.

Arguments:

WF_ID [required]

beeflow reexecute: Reexecute an archived workflow.

Arguments:

WF_ID [required]

Generating and Managing Configuration Files

You can use the beeflow config sub-command to configure BEE for your workflows. The following are further options for this sub-command:

beeflow config validate: Validate an existing configuration file.

beeflow config info: Display some info about bee.conf’s various options.

beeflow config new: Create a new config file.

beeflow config show: Show the contents of current bee.conf.