GeneNetwork

This repository contains the source code for the GeneNetwork (GN) server http://gn2.genenetwork.org/ (version 2 aka GN2). GN is a Web 2.0 style framework with included tools for doing genetics online using high-throughput data. GN is used for a wide range of studies. An exhaustive list of publications mentioning GN and its previous incarnation WebQTL can be found here.

Install

The recommended installation is with GNU Guix which allows you to deploy GN2 and dependencies as a self contained unit on any machine. The database can be run separately as well as the source tree (for developers). See the installation docs.

Run

Once installed GN2 can be run online through a browser interface

genenetwork2

(default is http://localhost:5003/). A quick example is

env GN2_PROFILE=~/opt/gn-latest SERVER_PORT=5300 GENENETWORK_FILES=~/data/gn2_data/ ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-dev

For full examples (you may need to set a number of environment variables), including running scripts and a Python REPL, also see the startup script ./bin/genenetwork2.

Also Mysql and Elasticsearch need to be running, see INSTALL.

Testing

We are building 'Mechanical Rob' automated testing using Python requests which can be run with something like

env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ../test/requests/test-website.py -a http://localhost:5003

The GN2_PROFILE is the Guix profile that contains all dependencies. The ./bin/genenetwork2 script sets up the environment and executes test-website.py in a Python interpreter. The -a switch says to run all tests and the URL points to the running GN2 http server.

Documentation

User documentation can be found here. The architecture of the software stack is described here. The database schema is (still) shared with GN1 and currently described here. Software documentation is being expanded in the source code repository.

Contributing

Issues can be raised through github.

Contribute to GN2 source code by forking the github repository with git and sending us pull requests.

For development GN2 has a mailing list and an active IRC channel #genenetwork on freenode.net with a web interface.

License

The GeneNetwork2 source code is released under the Affero General Public License 3 (AGPLv3). See LICENSE.txt.

More information

For more information visit http://www.genenetwork.org/

Cite

GeneNetwork was published in the Journal of Open Source Software as 'GeneNetwork: framework for web-based genetics' by Zachary Sloan, Danny Arends, Karl W. Broman, Arthur Centeno, Nicholas Furlotte, Harm Nijveen, Lei Yan, Xiang Zhou, Robert W. WIlliams and Pjotr Prins

You may also cite the software using

.

Contact

IRC on #genenetwork on irc.freenode.net.

Code and primary web service managed by Dr. Robert W. Williams and the University of Tennessee Health Science Center, Memphis TN, USA.