#+TITLE: Installing GeneNetwork services

* Table of Contents                                                     :TOC:
 - [[#introduction][Introduction]]
 - [[#source-deployment][Source deployment]]
   - [[#install-guix][Install guix]]
   - [[#checkout-the-git-repositories][Checkout the git repositories]]
   - [[#update-guix][Update guix]]
   - [[#install-gn2][Install GN2]]
   - [[#run-gn2][Run GN2]]
   - [[#run-mysql-server][Run MySQL server]]
   - [[#run-your-own-copy-of-gn2][Run your own copy of GN2]]
 - [[#source-deployment-and-other-information-on-reproducibility][Source deployment and other information on reproducibility]]

* 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 [[https://github.com/pjotrp/guix-notes/blob/master/README.md][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 [[https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest][Guix bioinformatics]] and [[https://github.com/genenetwork/guix/tree/gn-latest][GNU Guix main]].

* Source deployment
** Install guix

Deploying from source is also straightforward. Install GNU Guix using
a binary tar ball as described [[https://github.com/pjotrp/guix-notes][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:

#+begin_src bash
cd ~
mkdir genenetwork
cd genenetwork
git clone --branch gn-latest https://github.com/genenetwork/guix-bioinformatics 
git clone --recursive --branch gn-latest https://github.com/genenetwork/guix guix-gn-latest
cd guix-gn-latest
#+end_src bash

** 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
[[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix][these]] steps carefully.

** Install GN2

#+begin_src bash
env GUIX_PACKAGE_PATH=../guix-bioinformatics/ ./pre-inst-env guix package -i genenetwork2 --fallback 
#+end_src bash

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

#+begin_src bash
./pre-inst-env guix package --search-paths
#+end_src bash

** Run GN2

After setting the paths for the server

#+begin_src bash
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"
#+end_src bash

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

#+begin_src bash
genenetwork2
#+end_src bash

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]].