Galaxy 설치

0. OS 설치
http://ctrlcv.co.cc/entry/CentOSX8664-62-설치

 

 

1. galaxy 사용자 생성

root # useradd galaxy
root # passwd galaxy

 

 

2. virtualenv 설치

root # easy_install pip
root # pip install virtualenv

 

 

3. Mercurial Distributed SCM 설치

root # yum -y install mercurial

 

 

4. Galaxy 기본 설치

root # mkdir /share/apps/galaxy-dist
root # chown -R galaxy.galaxy /share/apps/galaxy-dist
root # su - galaxy
galaxy $ cd /share/apps
galaxy $ hg clone https://bitbucket.org/galaxy/galaxy-dist/  ### Get the latest copy from the repository

 

root # mkdir /share/apps/local
root # chown -R galaxy.galaxy /share/apps/local
root # su - galaxy
galaxy $ cd /share/apps
galaxy $ virtualenv --no-site-packages local

The --no-site-packages flag is deprecated; it is now the default behavior.
New python executable in local/bin/python
Installing setuptools............done.
Installing pip...............done.

galaxy $ source ./local/bin/activate 

 

 

5. Using mysql

# mysql -u root -p

mysql> create database galaxy;
Query OK, 1 row affected (0.00 sec)

mysql> use galaxy;
Database changed
mysql> grant all on galaxy.* to 'galaxy'@'%' identified by '패스워드';
mysql> grant all on galaxy.* to 'galaxy'@'localhost' identified by '패스워드';

 

6. universe_wsgi.ini

root # su - galaxy
galaxy $ cd /share/apps/galaxy-dist
galaxy $ cp /share/apps/galaxy_dist/universe-wsgi.ini.sample /share/apps/galaxy-dist/universe_wsgi.ini
galaxy $ vi universe_wsgi.ini
#admin_users = None
admin_users = isbyeon@kribb.re.kr

 

#host = 127.0.0.1
host = 0.0.0.0

#cleanup_job = always
cleanup_job = never

#database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE
database_connection = mysql://galaxy:kobic123@galaxy.kobic.kr/galaxy

#start_job_runners = None
start_job_runners = drmaa

#environment_setup_file = None
environment_setup_file = True

#default_cluster_job_runner = local:///
default_cluster_job_runner = drmaa://-q galaxy -V/

### drmaa://-l mem=4gb:nodes=1:ppn=6/
### This should request 4gb of memory on a single node with 6 threads

 

 

7. 데몬 스타팅...

# vi /etc/profile.d/drmaa.sh
export DRMAA_LIBRARY_PATH=/opt/gridengine/lib/lx26-amd64/libdrmaa.so.1.0

# chmod 755 /share/apps/galaxy-dist/run.sh
# vi /etc/init.d/galaxy

#!/bin/bash
. /etc/rc.d/init.d/functions
. /etc/profile.d/drmaa.sh ### DRMAA_LIBRARY_PATH
. /etc/profile.d/sge-binaries.sh ### $SGE_ROOT

GALAXY_USER=galaxy
GALAXY_DIST_HOME=/share/apps/galaxy-dist
GALAXY_RUN="${GALAXY_DIST_HOME}/run.sh"
GALAXY_PID="${GALAXY_DIST_HOME}/paster.pid"

 

case "$1" in
start)
echo -n "Starting galaxy services: "
daemon --user $GALAXY_USER "${GALAXY_RUN} --daemon --pid-file=${GALAXY_PID}"
touch /var/lock/subsys/galaxy
;;
stop)
echo -n "Shutting down galaxy services: "
daemon --user $GALAXY_USER "${GALAXY_RUN} --stop-daemon"
rm -f /var/lock/subsys/galaxy
;;
status)
daemon --user galaxy "${GALAXY_RUN} --status"
;;
restart)
$0 stop; $0 start
;;
reload)
$0 stop; $0 start
;;
*)
echo "Usage: galaxy {start|stop|status|reload|restart"
exit 1
;;
esac

# chmod 755 /etc/init.d/galaxy
# service galaxy restart

 

 

8. Galaxy tools 설치

1. fastx_toolskit 설치

 

# mkdir /share/apps/galaxy-tools
# chown -R galaxy.galaxy galaxy-tools
# su - galaxy
$ cd ~/src/
$ wget http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_galaxy_files.tar.bz2
$ tar jxvfp fastx_toolkit_0.0.13_galaxy_files.tar.bz2
$

# vi /share/apps/galaxy-dist/galaxy-setting.sh
# chmod 755 /share/apps/galaxy-dist/galaxy-setting.sh
# ln -s /share/apps/galaxy-dist/galaxy-setting.sh /etc/profile.d/galaxy-setting.sh

 

 

 

 

 

(작성중)....
An error occurred running this job: Traceback (most recent call last):
 File "/share/apps/galaxy-dist/tools/stats/gsummary.py", line 4, in <module>
 from rpy import *
ImportError: No module named rpy

 

 

참조 :

http://www.agapow.net/science/bioinformatics/galaxy/installing-galaxy