GBrowse Administration

Overview

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 and configure these servers.

Hardware Topology

The GBrowse topology looks like this:

 Master
 ------------- -----------------------------
 |    gb1    |              \               \
 |           |        -------------    -------------   
 |* * * * * *| <----- |    gb2    |    |    gb2    |   Slaves
 -------------        -------------    -------------  

Where:

 * * * * * = relational databases running under mysql on gb1.
      

Node Configuration

Create groups

sudo addgroup wormbase
sudo addgroup gbrowse
# Add yourself to the groups
sudo usermod -a -G gbrowse, wormbase tharris

Create Directories

Create a directory for GBrowse. For now, we're maintaining GBrowse on dedicated hardware completely distinct from the rest of the web application. This makes updates significantly easier, although it increases maintenance (ie of boilerplate). We'll also keep gbrowse inside a wormbase/ directory should we wish to install other components on these servers at a later date.

Let $ROOT = /usr/local/wormbase

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

Debian preparation

$ sudo apt-get update
$ sudo apt-get install gcc

Install Perl 5.10.1 or greater

You'll need Perl version 5.10.1 or greater.

Debian:

$ sudo apt-get install perl

Or from source:

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
  // Or, to install in a local path:
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}

Install Apache

On Debian (including it's annoying directory layout)

$ sudo apt-get install apache2

Or from source

Install MySQL > 5.1

We need a newer version of mysql than is available from the package manager. We'lll install the binary for x86_64.

For now, only the master server will run mysql. In the future, each dedicated slave could as well in order to meet growing demand.

$ groupadd mysql
$ useradd -g mysql mysql
$ usermod -a -G mysql tharris
$ cd /usr/local
$ sudo gunzip < /path/to/mysql-VERSION-OS.tar.gz | sudo tar xvf -
$ sudo ln -s full-path-to-mysql-VERSION-OS mysql
$ cd mysql
$ sudo chown -R mysql .
$ sudo chgrp -R mysql .
$ sudo scripts/mysql_install_db --user=mysql  // may be necessary to remove /etc/mysql/my.cnf first
$ sudo chown -R root .
$ sudo chown -R mysql data
$ sudo chmod 2775 data // I like to be able to write to my datadir

// Copy the configuration file
$ sudo cp support_files/my-medium.cnf /etc/my.cnf

// Set up mysql to start up automatically
$ sudo cp support_files/mysql.server /etc/init.d/.
$ cd /etc/rc3.d
$ sudo ln -s ../init.d/mysql.server S90mysql
$ cd ../rc5.d
$ sudo ln -s ../init.d/mysql.server S90mysql

// Start it up and set a root password.
$ sudo /etc/init.d/mysql.server start
$ mysqladmin -u root password 'PASSWORD'

Install Requisite Perl Modules

All libraries specific for GBrowse are maintained in a local directory, specific to the version of gbrowse being run. This means that prerequisites need to be installed for each version of Gbrowse.

$ cd /usr/local/wormbase
$ mkdir gbrowse-2.01  // eg
$ ln -s gbrowse-2.01 gbrowse-current
$ mkdir gbrowse-current/extlib

Install local::lib to make things easier:

$ sudo perl -MCPAN -e 'CPAN::install(local::lib)'
$ cd /usr/local/wormbase/gbrowse-current/extlib

To install modules to this path:

$ perl -Mlocal::lib=.
$ eval $(perl -Mlocal::lib=--self-contained,./)
$ sudo rm -rf ~/.cpan
$ perl -MCPAN -e shell

// You need libexpat first. On debian:
$ sudo apt-get install expat libexpat1 libexpat1-dev

cpan> install Bio::Perl        // may be necessary to install from source
cpan> install Bio::Graphics    // may be necessary to install from source

GD can be problematic:

$ sudo apt-get install libgd2-noxpm libgd2-noxpm-dev
cpan> install GD GD::SVG