Installing BioPerl on Ubuntu Server

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For the generic instructions, see: Installing BioPerl on Unix.

Version: Ubuntu Server 6.0.6

Everything below was done as user root. To open a root shell under Ubuntu, login as a normal user, then type 'sudo su -'.


Quick and dirty notes:

Contents

Install and Configure a Basic Ubuntu Server

Do install then configure.

apt-get clean
apt-get update
apt-get upgrade
apt-get install ssh screen
apt-get clean


Install as much as possible with apt-get

Enable Universe and Multiverse in /etc/apt/sources.list

apt-get update
apt-get install \
 lynx unzip zip ncftp gcc libc6-dev make mysql-server apache2 \
 perl libgd-gd2-perl libcgi-session-perl libclass-base-perl libexpat1-dev
apt-get clean


Install CPAN and perl modules not available via apt-get

cpan -i 'Text::Shellwords'  # choose defaults if first time


Install BioPerl

cd /tmp
wget -N http://bioperl.org/DIST/current_core_unstable.tar.bz2
tar -xjvf current_core_unstable.tar.bz2
cd bioperl-*
perl Build.PL   # choose the defaults
./Build test
./Build install

Install GBrowse

cd /tmp/
url='http://superb-west.dl.sourceforge.net/sourceforge/gmod/'
wget "${url}/Generic-Genome-Browser-1.66.tar.gz"
tar -xzvf Generic-Genome-Browser-*.tar.gz
cd /tmp/Generic-Genome-Browser-*
make clean
perl Makefile.PL \
 CONF=/etc/apache2/ \
 HTDOCS=/var/www/ \
 CGIBIN=/usr/lib/cgi-bin/
make
make test
make install
chown -R bioinfo.bioinfo /var/www/gbrowse/
chmod g+w /var/www/gbrowse/databases/
chown -R bioinfo.bioinfo /etc/apache2/gbrowse.conf/
chmod g+w /etc/apache2/gbrowse.conf/

Tests

mysql --no-defaults -h localhost -e status
lynx -dump http://localhost
perl -e ';' -MCGI
perl -e ';' -MGD
perl -e ';' -MCGI::Session
perl -e ';' -MDBI
perl -e ';' -MDBD::mysql
perl -e ';' -MDigest::MD5
perl -e ';' -MText::Shellwords
perl -e ';' -MClass::Base
perl -e ';' -MBio::Seq
lynx -dump http://localhost/gbrowse
lynx -dump http://localhost/cgi-bin/gbrowse/yeast_chr1
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