Difference between revisions of "Gbrowse on 4.0.2CD"
From Knoppix Documentation Wiki
(gbrowse on 4.0.2CD) |
(basic gbrowse) |
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| Line 1: | Line 1: | ||
| + | Code to install a basic gbrowse environment | ||
<pre><nowiki>#!/bin/bash | <pre><nowiki>#!/bin/bash | ||
| Line 9: | Line 10: | ||
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 | + | 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' | + | 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 | ||
| Line 20: | Line 21: | ||
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
)
