Galaxy

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Galaxy
General
Version 2013.06.03
Stable 2013.06.03
Function Life Sciences Software
Files
Config File /home/galaxy/galaxy-dist/universe_wsgi.ini
Log File /home/galaxy/galaxy-dist/paster.log
Scripts
Start su - galaxy -c ". ./galaxy_env/bin/activate; cd galaxy-dist/; sh run.sh --daemon"

Bioinformatics Workflow Management System.

Contents

General

  • Version: hg heads (Run as the galaxy user from /home/galaxy/galaxy-dist)
  • Start:
su - galaxy
 
. ./galaxy_env/bin/activate
 
cd galaxy-dist/
 
sh run.sh --daemon
  • Stop:
su - galaxy
 
. ./galaxy_env/bin/activate
 
cd galaxy-dist/
 
sh run.sh --daemon stop

Installing Galaxy

# Install Mercurial.
yum install mercurial
 
useradd galaxy
passwd galaxy
# Password.
 
su - galaxy
 
hg clone https://bitbucket.org/galaxy/galaxy-dist/
 
# Install virtualenv to have an isolated Python environment.
wget http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py
python virtualenv.py --no-site-packages galaxy_env
. ./galaxy_env/bin/activate
 
# Run the galaxy server. If this is the first time galaxy is run, lots of modules will be downloaded.
cd galaxy-dist/
sh run.sh --reload
####### Stop the server with Ctrl-C. #######
 
# Edit the configuration file /home/galaxy/galaxy-dist/universe_wsgi.ini
# Change the settings below to the values:
# debug = False
# use_interactive = False
 
# Use PostgreSQL as database.
 
su - postgres
psql
CREATE USER galaxy;
# Password is the same password as the Linux galaxy user. Needed???
ALTER USER galaxy WITH ENCRYPTED PASSWORD 'password';
ALTER DATABASE galaxy OWNER TO galaxy;
 
\q
 
su - galaxy
# Edit the configuration file /home/galaxy/galaxy-dist/universe_wsgi.ini
### database_connection = postgres:///galaxy?user=galaxy&password=password?host=/var/lib/postgresql
 
. ./galaxy_env/bin/activate
cd galaxy-dist/
 
# For testing only:
# sh run.sh --reload
# Ctrl-C to stop
 
# Running Galaxy as a daemon:
sh run.sh --daemon
 
# Using Nginx as web server.
# Configuration file /etc/nginx/conf.d/websitename.conf:
 
upstream galaxy_app {
    server localhost:8080;
}
 
server {
    listen       90;
    server_name  localhost;
 
    client_max_body_size 10G;
    location / {
        root                  /usr/share/nginx/html;
        index                 index.html index.htm;
        auth_basic            "Restricted";
        auth_basic_user_file  /path/to/file/with/passwords;
        proxy_pass            http://galaxy_app;
        proxy_set_header      X-Forwarded-Host $host;
        proxy_set_header      X-Forwarded-For  $proxy_add_x_forwarded_for;
    }
 
    error_page   500 502 503 504  /50x.html;
    location = /50x.html {
        root   /usr/share/nginx/html;
    }
}

Upgrade Galaxy

  • Valid for 26920e20157f to 40f1816d6857 to 17d57db9a7c0 to ec29ce8e27a1 to da9d740fce31 to whatever.
APPNAME=galaxy
DATE=`date +%Y-%m-%d`
BACKUPDIR=/home/backup/${APPNAME}/${APPNAME}_${DATE}
 
# Backup the configuration files.
# Create backup directory if it does not exist.
if [ ! -d "${BACKUPDIR}" ]
then
    mkdir -m 755 -p ${BACKUPDIR}
fi
cp -pr /home/galaxy/galaxy-dist/universe_wsgi.ini $BACKUPDIR/universe_wsgi.ini
 
# Stop Galaxy.
su - galaxy
. ./galaxy_env/bin/activate
cd galaxy-dist/
sh run.sh --daemon stop
 
RAWNEWVERSION=`curl -sd "action=ask&query=[[Galaxy]]|%3FStable&format=json" http://www.geilthings.com/api.php` 
NEWVERSION=`echo "$RAWNEWVERSION" | grep -Po '^.*?\K(?<=Stable\":\[\").*?(?=\")'`  
echo $NEWVERSION
# hg pull -u -r ${NEWVERSION}
hg pull
hg update release_${NEWVERSION}
 
# TODO. Check: The PostgreSQL server must be running.
sh manage_db.sh upgrade
 
# Start Galaxy.
sh run.sh --daemon
 
# Check new version.
# TODO. Check that output of 'hg heads' contains $NEWVERSION.
# Output of hg heads:
# changeset:   8525:a4113cc1cb5e
# tag:         tip
# ...
hg heads

Running Galaxy

Versions

Software name Version number Version date
Galaxy b5bda7a5c345
12fcd068b12e
5dcbbdfe1087
f364d992270c
36ad8aa7b922
a4113cc1cb5e
2013.02.08
2013.04.01
security_2013.04.08
2013.06.03
13 October 2012
24 October 2012
17 November 2012
8 December 2012
26 December 2012
11 January 2013
9 February 2013
6 April 2013
5 May 2013
  • 2013-February-09: Galaxy changed their version tag from an alphanumeric string to a date.

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