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Turn Galaxy Workflows into standalone scripts.

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mvdbeek/workflow2executable

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workflow2executable

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Turn Galaxy Workflows into standalone scripts.

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.

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Turn Galaxy Workflows into standalone scripts.

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