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.

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.

Once having installed GN2 it can be run 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 mariadb and redis need to be running, see INSTALL.

To have tests pass, the redis and mariadb instance should be running, because of asserts sprinkled in the code base(these will be removed in due time).

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

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.

To run unittests, first cd into the genenetwork2 directory:

# You can use the coverage tool to run the tests
# You could omit the -v which makes the output verbose
runcmd coverage run -m unittest discover -v

# Alternatively, you could run the unittests using:
runpython -m unittest discover -v

# To generate a report in wqflask/coverage_html_report/:
runcmd coverage html

The runcmd and runpython are shell aliases defined in the following way:

alias runpython="env GN2_PROFILE=~/opt/gn-latest TMPDIR=/tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ ./bin/genenetwork2

alias runcmd="time env GN2_PROFILE=~/opt/gn-latest TMPDIR=//tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ ./bin/genenetwork2 ./etc/default_settings.py -cli"

Replace some of the env variables as per your use case.

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.

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.

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

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

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

.

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.