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#+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 tend to get very complex. In this document we
explain the GeneNetwork 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 via a GNU Guix installation from a
checked out version of the Guix package tree (this is required for
reproducibility).
* 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]].
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