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-#+TITLE: Installing GeneNetwork services with GNU Guix
+#+TITLE: Installing GeneNetwork services
 
 * Table of Contents                                                     :TOC:
  - [[#introduction][Introduction]]
- - [[#binary-deployment][Binary deployment]]
- - [[#from-source-deployment][From source deployment]]
+ - [[#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 tend to get very complex. In this document we
-explain the GeneNetwork deployment system which is based on GNU Guix
-(see Pjotr's [[https://github.com/pjotrp/guix-notes/blob/master/README.md][Guix-notes]]).
+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.
 
-* Binary deployment
+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]].
 
-NYA
+* Source deployment
+** Install guix
 
-* From source deployment
+Deploying from source is also straightforward. Install GNU Guix using
+a binary tar ball as described [[https://github.com/pjotrp/guix-notes][here]].
 
-GNU Guix allows for [[https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org][reproducible deployment]] based on a checked out
-Guix repository - use gn-stable for that:
+If it works you should be able to install a package with
 
-#+begin_src sh   :lang bash
+: 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 checkout https://github.com/genenetwork/guix.git gn-stable-guix
-git checkout https://github.com/genenetwork/guix-bioinformatics.git
-#+end_src
+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
+#+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. Assuming you have
+Guix and Genenetwork2 installed (as described above) clone the GN2
+repository from https://github.com/genenetwork/genenetwork2_diet
+
+Copy the paths into your terminal from (mainly so PYTHON_PATH and
+R_LIBS_SITE are set)
+
+: guix package --search-paths
+
+Inside the repository:
+
+: 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]].
+