Gbrowse on 4.0.2CD

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Revision as of 22:02, 13 October 2005 by Rwcitek (Talk | contribs)

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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

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.


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 '' || 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