Command line tool for running Galaxy workflows.
Project description
[](https://travis-ci.org/AAFC-MBB/GFlow) 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.
Installation
From the source directory:
$ pip install -r requirements.txt $ python setup.py install
Configuration
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
Usage
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
Tests
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 setup.py test
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