Simison's system notes for CCG Galaxy admins

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Table of Contents

Create an admin user 
    To give a user Galaxy admin privileges, add their Galaxy login ( email ) to the list in the following config setting in the Galaxy
    configuration file /data/galaxy/galaxy-dist/universe_wsgi.ini.
    use vi to edit the following line:
    
$ this should be a comma-separated list of valid Galaxy users
    admin_users = bsimison@calacademy.org, bernal.moises@gmail.com
Uploading directories of data 
    In order for CCG users to load their large data sets into the Galaxy history panel, I have set up a links directory /data/galaxy/links
    where users can create a symbolic  link to their data. These links will permit admin users to load the linked directories into their Galaxy
    datasets and then load them into their "histories" without moving or duplicating the original data.
    
$ sudo ln -s /data/simison/rad_tag_data /data/galaxy/links/wbs_rad_tag_data

    preface the link name with your intitials and do not chnage the name of the directory after you create the link :P
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