workflow2executable

Turn Galaxy Workflows into standalone scripts.

• Free software: MIT license
• Documentation: https://workflow2executable.readthedocs.io.

Turn Galaxy Workflows into standalone scripts.

Works only with regular dataset inputs for now. Might ultimately fit better into planemo.

The basic idea is that a workflow with completely defined input section describes itself:

workflow2executable 28d1e2d715476c2c https://usegalaxy.org --script_path workflow.py

Should create a python script that will run a workflow on a given Galaxy server. Useage can be seen with

python workflow.py --help

Usage: workflow.py [OPTIONS]

  Run Select last n lines workflow

Options:
  --input_dataset PATH
  --number_of_lines_to_keep INTEGER
  -a, --api_key TEXT              API key to use for running workflow
  -g, --galaxy_url TEXT           Galaxy URL to use for running workflow
                                  [default: https://usegalaxy.org]

  -h, --history_id TEXT           History ID that will contain workflow
                                  results

  -n, --new_history_name TEXT     Create a new history with this name. Will
                                  not be used if history ID is provided.

  --publish / --private           Publish history?
  --monitor_invocation / --no_monitor_invocation
                                  Print workflow invocation status updates?
  --workflow_id_override TEXT     Override workflow to run with this workflow
                                  id or uuid

  --quiet TEXT                    Decrease logging output
  --help                          Show this message and exit.

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.