AAFC-BICoE/gflow

Name: gflow

Owner: Biological Informatics CoE @ Agriculture and Agri-Food Canada

Owner: Biological Informatics CoE @ Agriculture and Agri-Food Canada

Description: Python command-line tool for running Galaxy workflows

Created: 2015-10-29 15:10:13.0

Updated: 2016-11-04 14:05:33.0

Pushed: 2016-11-07 18:37:54.0

Homepage: null

Size: 2539

Language: Python

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README

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_URLand ``GALAXY_API_KEY``` environment variables, execute the tests with:

$ python setup.py test

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_URLand ``GALAXY_API_KEY``` environment variables, execute the tests with:

$ python setup.py test