path: root/doc/README.org

#+TITLE: Installing GeneNetwork services

* Table of Contents                                                     :TOC:
 - [[#introduction][Introduction]]
 - [[#binary-deployment][Binary deployment]]
   - [[#install-guix-using-a-tar-ball][Install Guix using a tar ball]]
   - [[#fix-locale][Fix locale]]
   - [[#authorize-our-archives][Authorize our archives]]
   - [[#download-and-install-the-gn2-archive][Download and install the GN2 archive]]
 - [[#source-deployment][Source deployment]]
   - [[#install-guix][Install guix]]
   - [[#checkout-the-git-repositories][Checkout the git repositories]]
   - [[#run-guix-daemon][Run guix-daemon]]
   - [[#install-gn2][Install GN2]]
   - [[#run-gn2][Run GN2]]
   - [[#run-mysql-server][Run MySQL server]]
   - [[#other][Other]]
 - [[#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.

* Binary deployment

Note binary deployment is not working pending a few improvements
to GNU Guix. See source deployment instead.

** Install Guix using a tar ball

GN can be deployed either as a binary tarball or as a GNU Guix
package. First install GNU Guix following the instructions of the
[[https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html#Binary-Installation][binary installation]] using a tar ball from [[https://www.gnu.org/software/guix/download/][here]].

With guix-daemon running you should be able to install the hello
package:

: guix package -i hello

** Fix locale

You may want to 

#+begin_src sh   :lang bash
export GUIX_LOCPATH=$HOME/.guix-profile/lib/locale
export LC_ALL=en_US.utf8
#+end_src sh   :lang bash

** Authorize our archives

Next add our archive key to guix (as root):

#+begin_src scheme
echo "(public-key   
 (ecc 
  (curve Ed25519)
  (q #E9A95686D8437186302E07C7AB9BF3913F435026C2D389AF27D9C66FD6EBB649#)
  )
 )
"|guix archive --authorize
#+end_src scheme

if you have trouble finding a suitable guix try

: ls /gnu/store/*guix-*/bin/guix

and you should be able to use this directly, e.g.

: alias guix=/gnu/store/632msbms2yaldfnlrb5lbnlnmn9yjisw-guix-0.9.0/bin/guix
: guix --version

** Download and install the GN2 archive

Find the archive on 

  http://files.genenetwork.org/software/

download and install with

#+begin_src bash
guix archive --import < genenetwork2-data-hash.nar
#+end_src bash

and you should see a list of packages installing, e.g.

#+begin_src bash
importing path `/gnu/store/l1zs2drn3zdzl5ysjcmhibcpa35p9zfc-python2-mysqlclient-1.3.7'
importing path `/gnu/store/n7kfg4knibvblggy8ci2liscl7vz5wkg-python2-parallel-1.6.4'
importing path `/gnu/store/qvv16qwlq59gp5d07lwbf5n8ndsi3il3-python2-sqlalchemy-1.0.11'
importing path `/gnu/store/qw872mbmr9ir0a9drv9xw9pvjk05ywwy-python2-xlsxwriter-0.8.4'
importing path `/gnu/store/wc112m1xfy3p08v14bdzay2ki2rirdsm-pylmm-gn2-1.0-3c6d1cac8'
importing path `/gnu/store/zfkcy17c2ks3cd9ks14irdabqvmlfpyn-python2-flask-sqlalchemy-2.1'
importing path `/gnu/store/cgcjdiz1qylbc372gc3nda3372ihkpqb-genenetwork2-2.0-a8fcff4'
(etc.)
#+end_src bash

The following packages need to be added and the R path set

: export R_LIBS_SITE="/home/wrk/.guix-profile/site-library/"
: guix package -i /gnu/store/w0dqg9dshq53j8xhcnqgvnvms2s6y5k5-r-wgcna-1.49-425bc170cc0873ddbd414675ac40f6d4d724c7cb
: guix package -i /gnu/store/k60bdlm0v7xic88j2z5c1jb1jvc371mn-r-qtl-1.38-4

You can add the last one to your profile

: guix package -i /gnu/store/cgcjdiz1qylbc372gc3nda3372ihkpqb-genenetwork2-2.0-a8fcff
: export PATH=~/.guix-profile/bin:$PATH
: genenetwork2

 or run it directly with

: /gnu/store/cgcjdiz1qylbc372gc3nda3372ihkpqb-genenetwork2-2.0-a8fcff/bin/genenetwork2

* 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]].

** Checkout the git repositories

Check out the guix and guix-bioinformatics repositories:

#+begin_src bash
cd ~
mkdir genenetwork
cd genenetwork
git clone 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

** Run guix-daemon

At this 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
#+end_src bash

** Run GN2

#+begin_src bash
export PATH=~/.guix-profile/bin:$PATH
genenetwork2
#+end_src bash

will start the default server which listens on port 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';


** Other

Update guix with a 'guix pull' and make guix visible in the path.
More information exists also in my [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org][guix-notes]].

With guix running you should be able to install python, for example.

: guix package -i python2

This will make python appear in $HOME/.guix-profile/bin/python. Suggested
environment settings can be seen with

: guix package --search-paths



* Source deployment and other information on reproducibility

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