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 setup.py 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 setup.py test