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 info: Get information about beeflow, including .beeflow directory location, log location, and version number.

beeflow core stop: Stop running beeflow components. Active workflows will be paused. You may continue running paused workflows with the beeflow resume <wf_id> command. Once you start beeflow components after a stop, you should check the status of workflows, query any running workflows. If they were intializing when a beeflow core stop was issued, the workflow may be running with tasks stuck in the waiting state. If this occurs and you want the workflow to continue pause and resume the workflow (beeflow pause <wf_id>, beeflow resume <wf_id>) or to start over cancel the workflow (beeflow cancel <wf_id>) and resubmit it.

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

beeflow core reset: Stop the beeflow daemon and cleanup the bee_workdir directory to start from a fresh install.

Options:

--archive, -a, Backup logs, workflows, and containers in bee_workdir directory before removal. [optional]

beeflow core pull-deps: Pull BEE dependency containers

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 (if using CWL tarball), path of main CWL (if using CWL directory) [required]

  • YAML, filename of yaml file (if using CWL tarball), path of yaml file (if using CWL directory) [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]

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 remove: Remove cancelled or archived workflow and it’s information.

Arguments:

WF_ID [required]

beeflow copy: Copy an archived workflow.

Arguments:

WF_ID [required]

beeflow reexecute: Reexecute an archived workflow.

Arguments:

WF_ID [required]

beeflow dag: Export a directed acyclic graph (DAG) of a submitted workflow. This command can be run at any point of the workflow. To see the DAG of a workflow before it runs, submit the workflow with the --no-start flag and then use the dag command. The DAGs are exported to ~/.beeflow/dags. See Workflow Visualization for more information.

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.