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

Those who want to enable GBrowse's ability to produce high-resolution images and PDFs should install:

1. The GD::SVG module (from CPAN)
2. Inkscape

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.

#Utilities to help with fetching components distributed in source code
sudo apt-get install wget
sudo apt-get install cvs
sudo apt-get install subversion

#apache2
sudo apt-get install apache2

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

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

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

The Perl GD::SVG library is not currently distributed as a DEB package but can be installed from the CPAN shell (as root):

sudo perl -MCPAN -e 'install GD::SVG'

BioPerl is also not currently distributed as a DEB package and must 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
./Build test   # optional, but recommended; do not proceed if more than a few tests fail.
sudo ./Build install

The last step of the recipe must be executed as root (shown here using sudo). You're done installing prerequisites! You can now go back to the GBrowse 2.0 HOWTO and follow the installation instructions for your platform.

RPM Systems (yum)

This includes Fedora, RedHat, SuSE, Mandriva, PCLinuxOS, and CentOS. Most of these distributions have the command line package management tool yum which is used in the following command examples. These commands will need to be run as root (or equivalently by using sudo in the manner shown above):

#Utilities to help with fetching components distributed in source code
yum install wget
yum install cvs
yum install subversion

#apache2
yum install httpd

#libgd2 and its Perl library
yum install gd-devel
yum install perl-GD

#other Perl modules
yum install perl-Module-Build
yum install perl-CPAN
yum install perl-IO-String
yum install perl-CGI-Session
yum install perl-JSON perl-JSON-Any
yum install perl-libwww-perl

#optionally...
apt-get install mysql-server mysql-libs perl-DBD-MySQL
apt-get install postgresql postgresql-server perl-DBD-Pg
apt-get install mod_perl
apt-get install inkscape
apt-get install perl-GD-SVG

The current BioPerl RPM package is out of date and should 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
./Build test   # optional, but recommended; do not proceed if more than a few tests fail.
./Build install

The last step of the recipe must be executed as root. You're done installing prerequisites! You can now go back to the GBrowse 2.0 HOWTO and follow the installation instructions for your platform.

MacOSX

These instructions apply to Macintosh OSX version 10.5, using the fink binary installer. First, download and install Fink. Next open up the terminal window and type the following commands as the root user or with sudo (as shown):

#Utility to help components distributed in source code
sudo fink install wget

#libgd2 and its Perl library
sudo fink install gd2 gd2-bin
sudo perl -MCPAN -e 'install GD'

#other Perl modules
sudo perl -MCPAN -e 'install IO::String'
sudo perl -MCPAN -e 'install CGI::Session'
sudo perl -MCPAN -e 'install JSON'
sudo perl -MCPAN -e 'install JSON::Any'

#optionally.
sudo fink install mysql
'''more to come here'''
sudo perl -MCPAN -e 'install GD::SVG'

this section is unfinished

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