GBrowse Gentoo HOWTO

Prerequisites

Install Apache

Apache2 will now work on most systems with no problems, if it doesn't for you, section Common Problems might be helpful.

Start by emerging apache2: add "apache2" to your USE flags in make.conf and

 emerge apache -av

To start Apache2 run:

/etc/init.d/apache2 start

If you'd like to have have Apache2 start on boot run:

rc-update add apache2 default

Install Mysql (Optional, But highly recommended)

 emerge mysql -av

Or if you do not want mysql to be updated automatically with the system,

 emerge mysql -1

This will install mysql once without adding its ebuild into world namespace. So next time when you emerge -u world, mysql will be excluded from updating.

Create the initial mysql database

 emerge --config mysql

This will also inform you to set the root password of mysql database. If you have more than one version of mysql installed on your machine, please name it sepcifically like =dev-db/mysql-4.1.21

Installing GBrowse using net installer

Now we have a very convenient way to have Gbrowse and all its prerequisites, like latest leased version of bioperl, GD, which were absent from your computer installed.

Download the network installer script:Generic-Genome-Browser/bin/gbrowse_netinstall.pl

Make sure you have root privilege and run

 perl gbrowse_netinstall.pl

Then follow the instruction to complete installation. The default settings are suitable from most circumstances.

The only thing need to be noticed is that the installer uses wrong directories as apache default directories. When the question appears, you should change them to

 /var/www/localhost/htdocs
 /var/www/localhost/cgi-bin

You may go to the main page of Gbrowse to see more detailed instructions about netinstaller.

Installing GBrowse with Source File

This page or section needs to be edited. Please help by editing this page to add your revisions or additions.

I believe that the GBrowse net install script should work just fine on Gentoo as well--can someone try it out and let me know? Scott 09:10, 18 June 2007 (EDT)

Download GBrowse Source from

 http://prdownloads.sourceforge.net/gmod

You should be uncompressed and unpacked the source files.

Install GBrowse

Change to the directory which the source files have been uncompressed and unpacked. We will install GBrowse in the default directory "/var/www/localhost/htdocs/" and "/var/www/localhost/cgi-bin/". Following these command:

 perl Makefile.PL APACHE=/var/www/localhost/ CONF=/etc/apache2/ HTDOCS=/var/www/localhost/htdocs/ CGIBIN=/var/www/localhost/cgi-bin/ DO_XS=1
 make 
 make install

Starting GBrowse

Start mysql and apache

 /etc/init.d/mysql start
 /etc/init.d/apache2 start

Now browse the documentation and example database at http://localhost/gbrowse.

AUTHORS

Copyright 2007, Tao Zhang <forrest_zhang(AT)163.com>(please change '(AT)' to '@').