Difference between revisions of "Gbrowse on 4.0.2CD"


From Knoppix Documentation Wiki
Jump to: navigation, search
(basic gbrowse)
m (prereqs)
Line 1: Line 1:
 +
 +
Prerequisits: a persistent disk image of about 300 MB.  I used 500 MB just to be sure I had enough room for temporary files and the like.
 +
 
Code to install a basic gbrowse environment
 
Code to install a basic gbrowse environment
 
<pre><nowiki>#!/bin/bash
 
<pre><nowiki>#!/bin/bash

Revision as of 21:58, 13 October 2005

Prerequisits: a persistent disk image of about 300 MB. I used 500 MB just to be sure I had enough room for temporary files and the like.

Code to install a basic gbrowse environment

#!/bin/bash

set -x

die () {
  echo "$1"
  exit $2
}

apt-get update || die "unable to apt-get" 1
apt-get -y install libcgi-perl libgd-gd2-perl libdbi-perl \
  libdbd-mysql-perl libmd5-perl libtext-shellwords-perl bioperl || die "unable to install " 2

cd /root
wget 'http://umn.dl.sourceforge.net/sourceforge/gmod/Generic-Genome-Browser-1.62.tar.gz' || die "unable to wget" 3
tar -xzvf Generic-Genome-Browser-1.62.tar.gz  || die "unable to untar" 4

( cd Generic-Genome-Browser-1.62/ &&
perl Makefile.PL CONF=/etc/apache/ HTDOCS=/var/www/ CGIBIN=/usr/lib/cgi-bin/ &&
make &&
make install || die "unable to install gbrowse" 5
)