setting up PostgreSQL database for Galaxy

RETURN to CCG Ubuntu Directory

Table of Contents

Dec. 30, 2012 
Install PostgreSQL 9.1
  
    To install the latest PostgreSQL:
    
$ sudo apt-get install postgresql
Dec. 30, 2012 
PostgreSQL server setup
    
    first set up the PostgreSQL postgres user password:
    
$ sudo -u postgres psql postgres
$ \password postgres
and give the password "postgres" when prompted.
Dec. 1, 2012 
Create database for Galaxy
  
    To set up a database for Galaxy, I installed pgAdminIII, a GUI interface to manage PostgreSQL.
    
$ sudo apt-get install pgadmin3
From the pgAdminIII tool I created a database named "galaxy" and made 'postgres' the owner.
Dec. 1, 2012 
Configure PostgreSQL for Galaxy
  
    PostgreSQL installs config files in /etc/postgresql/9.1/main. And data in /var/lib/postgresql/9.1/main.
    I edited the postgres pg_hba.conf file to allow everyone access from the CCG Ubuntu server.
    
$ sudo vi /etc/postgresql/9.1/main/pg_hba.conf
    edit the commented out lines as follows:
local   all         all                               trust
host    all         all         127.0.0.1/32          trust
host    all         all         ::1/128               trust
host    all         all         0.0.0.0/0             md5

    Edit the 'postgresql.conf file to allow connection from all computers: Change and uncomment "listen_addresses = 'localhost'"  to "listen_addresses = '*'".

listen_addresses = '*'
Dec. 1, 2012 
Configure Galaxy to connect to PostgreSQL
  
    Galaxy must be configured to communicate with the PostgreSQL database.
    Edit the universe_wsgi.ini file in /data/galaxy/galaxy-dist.
    I made the following changes:
admin_users = bsimison@calacademy.org
host = 10.5.10.18 [IP ADDRESS]
database_connection = postgres://postgres:postgres@localhost:5432/galaxy
Dec. 6, 2012 
Setting up auto start for Galaxy server
    To get Galaxy server to start automatically, use the Ubuntu "init.d" system. In the /data/galaxy/galaxy-dist/contrib directory is a
    sample init file "galaxy.debian-init" that needs to be editied and copied to the /etc/init.d directory. The edited lines are highlighted
    in red:
#!/bin/bash

# Author: James Casbon, 2009

### BEGIN INIT INFO
# Provides:             galaxy
# Required-Start:       $network $local_fs $mysql
# Required-Stop:
# Default-Start:        2 3 4 5
# Default-Stop:         0 1 6
# Short-Description:    Galaxy
### END INIT INFO

. /lib/lsb/init-functions

USER="galaxy"
GROUP="nogroup"
DIR="/data/galaxy/galaxy-dist/"
PYTHON="/usr/bin/python"
OPTS="-ES ./scripts/paster.py serve --log-file /home/galaxy/galaxy.log universe_wsgi.ini"
PIDFILE="/var/run/galaxy.pid"

case "${1:-''}" in
  'start')
           log_daemon_msg "Starting Galaxy"
           if start-stop-daemon --chuid $USER --group $GROUP --start --make-pidfile \
	             --pidfile $PIDFILE --background --chdir $DIR --exec $PYTHON -- $OPTS; then
             log_end_msg 0
           else
             log_end_msg 1
	   fi

        ;;
  'stop')
           log_daemon_msg "Stopping Galaxy" 
	   if start-stop-daemon --stop --pidfile $PIDFILE; then
	     log_end_msg 0
	   else 
	     log_end_msg 1
	   fi
        ;;
  'restart')
           # restart commands here
	   $0 stop
	   $0 start
			   
        ;;
  *)      # no parameter specified
        echo "Usage: $SELF start|stop|restart|reload|force-reload|status"
        exit 1
        ;;
esac    

    Then run the command to add entries to the rc*.d directories to start Galaxy at startup:
    
$ update-rc.d galaxy defaults