GBrowse 2.0 Prerequisites

Before installing GBrowse, you will need to install some prerequisites on your system. Most prerequisites come as prepackaged binaries which can be installed from the command line or via GUI tools. This document describes the prerequisites for Linux, Mac OSX, and Microsoft Windows systems.

Linux systems

The following prerequisites are needed to run GBrowse on Linux systems:

1. The Apache2 web server
2. Perl 5.8 or higher
3. The libgd2 library
4. The BioPerl "live" distribution
5. The following standard Perl libraries (available from CPAN)
   1. Module::Build
   2. GD
   3. JSON
   4. LWP
   5. Storable
   6. IO::String
   7. File::Temp
   8. Digest::MD5
   9. CGI::Session

In addition, although not required for a basic installation, you will probably want at least one relational database backend. One or both of:

1. MySQL
2. PostgreSQL

Those who want to obtain the best performance should consider the mod_perl addon to Apache:

1. mod_perl

You can install these prerequisites from source code, or if you use a modern Linux distribution, most are available as binary packages. There are two common package managers, Debian (DEB) and RedHat Package Manager (RPM). The next section shows you how to use command-line package management tools to install the prerequisites:

DEB Systems (apt)

Distributions on which apt is installed by default include Ubuntu (and its variants), Debian, and Mint. To install all prerequisites except for BioPerl, run the following commands as the root or using sudo (comments begin with the # sign). Some of these packages may already be installed on your system.

#get source code control systems in order to get BioPerl and GBrowse in later steps
apt-get install cvs
apt-get install subversion

#get apache2
apt-get install apache2

#get libgd2 and its Perl library
apt-get install libgd2-noxpm-dev
apt-get install libgd-gd2-perl

#get other Perl modules
apt-get install libmodule-build-perl
apt-get install libio-string-perl
apt-get install cgi-session-perl
apt-get install libwww-perl
apt-get install libjson-perl libjson-any-perl

#optionally...
apt-get install mysql-server mysql-client libdbd-mysql-perl
apt-get install postgresql
apt-get install libapache2-mod-perl2 libdbd-pg-perl

BioPerl is not currently distributed as a binary package and will need to be installed from source:

wget http://www.bioperl.org/DIST/nightly_builds/bioperl-live.tar.gz 
tar zxvf bioperl-live.tar.gz
cd bioperl-live
perl Build.PL
./Build
sudo ./Build install

The last step of the recipe must be executed as root (shown here using sudo).

Yum Package Manager

(yum)

This includes Fedora, RedHat, SuSE (YaST), Mandriva (Rpmdrake), PCLinuxOS (apt), CentOS,