1.) Create user called galaxy with password galaxy
admin@myserver:~# adduser galaxy
Adding user `galaxy' ...
Adding new group `galaxy' (1007) ...
Adding new user `galaxy' (1008) with group `galaxy' ...
Creating home directory `/home/galaxy' ...
Copying files from `/etc/skel' ...
Enter new UNIX password:
Retype new UNIX password:
passwd: password updated successfully
Changing the user information for galaxy
Enter the new value, or press ENTER for the default
Full Name []:
Room Number []:
Work Phone []:
Home Phone []:
Other []:
Is the information correct? [Y/n] Y
admin@myserver:~#
2.) Change user to galaxy and clone galaxy production version
admin@myserver: su galaxy
galaxy@myserver:/home/admin$ cd
galaxy@myserver: hg clone https://bitbucket.org/galaxy/galaxy-dist
3.) If you don't have mercurial client for clone galaxy use following step
admin@myserver:sudo apt-get install mercurial
4.) Set the $TEMP environment variable to Galaxy's new_files_path directory
galaxy@myserver:~$ export TEMP=/home/galaxy/galaxy-dist/database/tmp
5.) We need clean python interpreter with correct python path
galaxy@myserver:wget http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py
galaxy@myserver:/usr/bin/python2.6 virtualenv.py --no-site-packages galaxy_env
6.) Now we need to setup new database for galaxy.I am going to create PostgreSQL database
galaxy@myserver:~/galaxy-dist$ psql -h localhost -d postgres -U postgres
postgres=#CREATE DATABASE galaxy_prod;
postgres=# CREATE USER galaxy_prod_user WITH PASSWORD 'galaxy';
postgres=# GRANT ALL PRIVILEGES ON DATABASE galaxy_prod to galaxy_prod_user;
postgres=# \q
7.) Then we need to configure Galaxy default server settings to our server details
galaxy@myserver:cd galaxy-dist/
galaxy@myserver:~/galaxy-dist$ chmod -R 777 universe_wsgi.ini
galaxy@myserver:~/galaxy-dist$ vi universe_wsgi.ini
8.) Here is the basic changes for universe_wsgi.ini file.
host = xxx.xxx.23.123 [IP ADDRESS]
debug = False
use_interactive = False
database_connection = postgres://galaxy_prod_user:galaxy@localhost:5432/galaxy_prod
9.) There are many more changes we can do for galaxy by customizing niverse_wsgi.ini for instance adding tracks,user privileges, ftp upload e.t.c.Galaxy has its own server but there are pages with static contents therefore we can setup proxy to enhance efficiency
admin@myserver:vi /etc/httpd/conf/httpd.conf
10.) Add following lines to httpd.conf
<VirtualHost *:80>
ServerName xxx.xxx.23.123 [IP ADDRESS]
RewriteEngine on
#RewriteLog "/etc/httpd/logs/rewrite_log"
#RewriteLogLevel 9
RewriteRule ^/galaxy$ /galaxy/ [R]
#RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]
#RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L]
#RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L]
#RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L]
#RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L]
RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]
</VirtualHost>
11.) Now we need to restart proxy server.
admin@myserver:/etc/init.d/httpd restart
12.) Finally we can run galaxy
galaxy@myserver:~/galaxy-dist$ sh ./run.sh --daemon
13.) We can stop or see the status by using following commands
galaxy@myserver:~/galaxy-dist$ sh ./run.sh --stop-daemon
galaxy@myserver:~/galaxy-dist$ sh ./run.sh --status
14.) Done!
