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GBrowse Gentoo HOWTO

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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

Install Bioperl

The advantage of this approach is it's stepwise, so it's easy to stop and analyze in case of any problem.

Download, then unpack the appropriate package. For example:

>gunzip bioperl-1.5.2_102.tar.gz
>tar xvf bioperl-1.5.2_102.tar
>cd bioperl-1.5.2_102

Now issue the build commands:

>perl Build.PL
>./Build test

If you've installed everything perfectly and all the network connections are working then you may pass all the tests run in the './Build test' phase. It's also possible that you may fail some tests. Possible explanations: problems with local Perl installation, network problems, previously undetected bug in Bioperl, flawed test script, problems with CGI script using for sequence retrieval at public database, and so on. Remember that there are over 800 modules in Bioperl and the test suite is running more than 12000 individual tests, a few failed tests may not affect your usage of Bioperl.

If you decide that the failed tests will not affect how you intend to use Bioperl and you'd like to install anyway, or if all tests were fine, do:

>./Build install

This is what most experienced Bioperl users would do. However, if you're concerned about a failed test and need assistance or advice then contact bioperl-l@bioperl.org.

To './Build install' you need write permission in the perl5/site_perl/source area (or similar, depending on your environment). Usually this will require you becoming root, so you will want to talk to your systems manager if you don't have the necessary privileges.

Cite from http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix.

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: gbrowse_netinstall.pl

I edit gbrowse_netinstall.pl file, change the the gbrowse download mirror to http://jaist.dl.sourceforge.net/sourceforge/gmod/, because the mirror is faster than others, download from China.

 use constant SOURCEFORGE_MIRROR1  => 'http://jaist.dl.sourceforge.net/sourceforge/gmod/';

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

 Apache conf directory? [/usr/local/apache/conf] /etc/apache2/
 Apache htdocs directory? [/usr/local/apache/htdocs] /var/www/localhost/htdocs/
 Apache cgibin directory? [/usr/local/apache/cgi-bin] /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

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

Tao Zhang <forrest_zhang@163.com>.