Latest revision as of 05:31, 15 July 2008

The Generic Genome Browser, GBrowse, is a combination of database and interactive web page for manipulating and displaying annotations on genomes.

Code to install a basic GBrowse environment

Prerequisites: 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.

#!/bin/bash

set -x

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

apt-get update || die "unable to apt-get" 1
apt-get -y install perl-doc 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
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
)

/etc/init.d/apache restart

Point your browser to http://localhost/gbrowse

To enable gbrowse to start at boot time:

update-rc.d apache start 40 2 3 4 5 . stop 60 0 1 6 .

Code to install an intermediate gbrowse environment

Perform a basic install and then run the following code:

#!/bin/bash
set -x

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

apt-get update || die "unable to apt-get" 1

# XML::Parser, XML::Writer, XML::Twig, XML::DOM, LWP, GD::SVG
apt-get install libxml-parser-perl libxml-writer-perl libxml-twig-perl \
  libxml-dom-perl libwww-perl

# don't have this quite down yet