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Installing GeneNetwork services

Table of Contents

Introduction

Large system deployments can get very complex. In this document we explain the GeneNetwork version 2 (GN2) reproducible deployment system which is based on GNU Guix (see also Pjotr’s Guix-notes). The Guix system can be used to install GN with all its files and dependencies.

The official installation path is from a checked out version of the main Guix package tree and that of the Genenetwork package tree. Current supported versions can be found as the SHA values of ‘gn-latest’ branches of Guix bioinformatics and GNU Guix main.

Source deployment

Install guix

Deploying from source is also straightforward. Install GNU Guix using a binary tar ball as described here.

If it works you should be able to install a package with

guix package -i hello

Checkout the git repositories

Check out the two relevant guix and guix-bioinformatics git repositories:

cd ~
mkdir genenetwork
cd genenetwork
git clone --branch gn-latest https://github.com/genenetwork/guix-bioinformatics
git clone --branch gn-latest --recursive https://github.com/genenetwork/guix guix-gn-latest
cd guix-gn-latest

Update guix

At some point you may decide to create, install and run a recent version of the guix-daemon by compiling the guix repository. Follow these steps carefully.

Install GN2

env GUIX_PACKAGE_PATH=../guix-bioinformatics/ ./pre-inst-env guix package -i genenetwork2 --fallback 

Note that you can use the genenetwork.org guix substitute caching server at http://guix.genenetwork.org (which speeds up installs significantly because all packages are pre-built).

Make a note of the paths with

./pre-inst-env guix package --search-paths

Run GN2

After setting the paths for the server

export PATH=~/.guix-profile/bin:$PATH
export PYTHONPATH="$HOME/.guix-profile/lib/python2.7/site-packages"
export R_LIBS_SITE="$HOME/.guix-profile/site-library/"
export GUIX_GTK3_PATH="$HOME/.guix-profile/lib/gtk-3.0"
export GI_TYPELIB_PATH="$HOME/.guix-profile/lib/girepository-1.0"
export XDG_DATA_DIRS="$HOME/.guix-profile/share"
export GIO_EXTRA_MODULES="$HOME/.guix-profile/lib/gio/modules"

run the main script (in ~/.guix-profile/bin)

genenetwork2

will start the default server which listens on port 5003, i.e., http://localhost:5003/.

Run MySQL server

At this point we require the underlying distribution to install and run mysqld.

Download one of

http://files.genenetwork.org/raw_database/ https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip

Check the md5sum.

After installation inflate the database binary in the MySQL directory (this is subject to change soon)

chown -R mysql:mysql db_webqtl_s/
chmod 700 db_webqtl_s/
chmod 660 db_webqtl_s/*

restart MySQL service (mysqld). Login as root and

mysql> show databases;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| db_webqtl_s        |
| mysql              |
| performance_schema |
+--------------------+

Set permissions and match password in your settings file below:

mysql> grant all privileges on db_webqtl_s.* to gn2@"localhost" identified by 'mysql_password';

Note that if the mysql connection is not working, try connecting to the IP address and check server firewall, hosts.allow and mysql IP configuration.

Run your own copy of GN2

At some point you may want to fix the source code. Clone the GN2 repository from https://github.com/genenetwork/genenetwork2_diet

Inside the repository:

git clone 
cd genenetwork2_diet
./bin/genenetwork2 

Will fire up your local repo http://localhost:5003/ using the settings in ./etc/default_settings.py

To override settings create your own from a copy of default_settings.py and pass it into GN2 with

./bin/genenetwork2 $HOME/my_settings.py

and everything should work (note the full path to the settings file). This way we develop against the exact same dependency graph of software.

Source deployment and other information on reproducibility

See the document GUIX-Reproducible-from-source.org.