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Command line tool for running Galaxy workflows.

Project description

[![Build Status](]( GFlow ========================

This is a command line interface application that allows datasets and a workflow to be specified in a config file and then have the workflow executed on an instance of Galaxy.


From the source directory:

$ pip install -r requirements.txt $ python install


Make a copy of the sample config file in config/ and set the parameters in it as desired:

$ cp config/config.yml.sample config/config.yml


Then, execute:

$ gflow config/config.yml

Or, if executing from the source directory without having installed the tool:

$ export PYTHONPATH=$PYTHONPATH:$PWD $ ./scripts/gflow config/config.yml


A small number of data files and workflow files have been included in data/ and workflow/ for testing purposes. After setting the `GALAXY_URL` and `GALAXY_API_KEY` environment variables, execute the tests with:

$ python test

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