GBrowse Administration

GBrowse is one of the central -- and most heavily used -- components of the WormBase site. To meet this demand, we use a number of dedicated servers using GBrowse's built in master/slave configuration. This document describes how to build these servers, how to configure GBrowse, and tips and tricks for maintenance.

Installation

Create Directories

Create a directory for GBrowse. For now, we're maintaining GBrowse distinct from the rest of the web application. This makes updates significantly easier.

Let $ROOT = /usr/local/wormbase

$ sudo mkdir -p ${ROOT}/gbrowse2
$ sudo chgrp -R wormbase $ROOT
$ sudo chmod 2775 $ROOT

Install Perl 5.10.1 or greater

You'll need Perl version 5.10.1 or greater. We recommend installing a local version of Perl and required libraries. This makes management dramatically easier. We keep our Perl with the webapp itself.

If you have sufficient privileges, you may wish to use your pre-installed system Perl.

bash> mkdir ~/website/perl
bash> cd ~/src
bash> curl -O http://www.cpan.org/src/perl-5.10.1.tar.gz
bash> cd ~/build
bash> tar xzf ../src.perl-5.10.1.tar.gz
bash> cd perl-5.10.1
bash> ./Configure -des -Dprefix=$HOME/website/perl/5.10.1
bash> make
bash> make test
bash> make install

Be sure to set up your your system to preferentially use this newly installed Perl:

bash> export PATH=~/wormbase/perl/5.10.1/bin:${PATH}