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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.

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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Python command-line tool for running Galaxy workflows

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