Installing BioPerl on Ubuntu Server
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[edit] Introduction
written by Robert Citek originally posted on BioPerl-L on Feb 7, 2007
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:
[edit] 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
[edit] 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 apt-get clean
[edit] Install CPAN and perl modules not available via apt-get
cpan -i 'Text::Shellwords' # choose defaults if first time
[edit] 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
[edit] 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/
[edit] 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
