Difference between revisions of "Gbrowse on 4.0.2CD"


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(gbrowse on 4.0.2CD)
 
(basic gbrowse)
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 +
Code to install a basic gbrowse environment
 
<pre><nowiki>#!/bin/bash
 
<pre><nowiki>#!/bin/bash
  
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apt-get update || die "unable to apt-get" 1
 
apt-get update || die "unable to apt-get" 1
apt-get install libcgi-perl libgd-gd2-perl libdbi-perl \
+
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
+
   libdbd-mysql-perl libmd5-perl libtext-shellwords-perl bioperl || die "unable to install " 2
  
 
cd /root
 
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
 
tar -xzvf Generic-Genome-Browser-1.62.tar.gz  || die "unable to untar" 4
  
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make &&
 
make &&
 
make install || die "unable to install gbrowse" 5
 
make install || die "unable to install gbrowse" 5
)</nowiki>
+
)</nowiki></pre>
</pre>
+

Revision as of 21:57, 13 October 2005

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
)