Turn Galaxy Workflows into standalone scripts.
Project description
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.
History
0.1.0 (2019-08-13)
First release on PyPI.
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