Difference between revisions of "GBrowse Ubuntu HOWTO"

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(Using apt-get just to get the prereqs)
(Using apt-get just to get the prereqs)
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Execute the command below will install gbrowse prerequisites without installing gbrowse itself :
 
Execute the command below will install gbrowse prerequisites without installing gbrowse itself :
 
   sudo apt-get build-dep gbrowse
 
   sudo apt-get build-dep gbrowse
All gbrowse prerequisites will be installed without installing gbrowse itself
+
 
  
 
Then, you can install apache2 and samtools if necessary
 
Then, you can install apache2 and samtools if necessary

Revision as of 14:16, 1 April 2018

NOTE: As of the 11.10 release of Ubuntu, there is a .deb package for GBrowse (it's usable on Debian machines as well, but I don't know the details of what repository needs to be activated to get GBrowse via apt-get on Debian).

ANOTHER NOTE: the current version of GBrowse in that deb package is fairly old (2.38 versus the current 2.55); below I'll outline using apt-get to get all of the prerequisites for GBrowse but use cpan to install GBrowse.

To install GBrowse on a recent Ubuntu distribution, just do this:

 sudo apt-get install gbrowse gbrowse-calign gbrowse-data libbio-samtools-perl apache2

And then point your browser at http://localhost/gbrowse2.

The content below will be left in place for older distributions.

Note: You may need to start the apache server once you have run the above installation

sudo /etc/init.d/apache2 start
  • If you plan to use a MySQL database, you may need to install mysql
sudo apt-get install mysql-server

Using apt-get just to get the prereqs

Execute the command below will install gbrowse prerequisites without installing gbrowse itself :

  sudo apt-get build-dep gbrowse


Then, you can install apache2 and samtools if necessary

 sudo apt-get install libbio-samtools-perl apache2

Then you can use the cpan shell to install GBrowse manually:

 cpan
 cpan> install Bio::Graphics::Browser2

This will still install a few perl modules, but it should go smoothly and quickly since most of the prerequisites will have been installed by the above apt-get command.

The information below is deprecated.

GBrowse does not have a .deb package, but many of its prerequisites are distributed in this way. This document describes how to install GBrowse on Ubuntu and other Linux distributions that use the Debian packaging system.

Prerequisites

Install Apache and Apache-modperl
 sudo apt-get install apache2
 sudo apt-get install libapache2-mod-perl2
 sudo apt-get install libapache2-mod-perl2-dev
 sudo apt-get install libapache2-mod-perl2-doc
 sudo apt-get install apache2-doc
Make the missing cgi-bin directory
 sudo mkdir /usr/lib/cgi-bin

This is not necessary for Ubuntu 7.10, as the Apache install creates it. For previous versions of Ubuntu, this did not happen.

Install libgd
 sudo apt-get install libgd2-dev

or

 sudo apt-get install libgd2-xpm-dev

for Ubuntu 7.10.

Install MySQL database (optional, but recommended)
 sudo apt-get install mysql-server
Install installer prereqs
 sudo apt-get install libarchive-zip-perl
 sudo apt-get install libarchive-tar-perl
 sudo apt-get install ncftp

Installing GBrowse with the Net Installer

Get the netinstaller script from SourceForge and save it to disk as "gbrowse_netinstall.pl". Then run:

sudo perl gbrowse_netinstall.pl

Be sure to double-check the paths that GBrowse guesses for the Apache configuration, htdocs, and cgibin directories, as these may have changed.

The script will download and install all the Perl modules on which GBrowse depends. During the installation process, some of these modules will ask you questions. You can almost always accept the defaults. If you change your mind later, you can simply run the script again.

When the installer is finished, you can browse the documentation and example database at http://localhost/gbrowse.

Author

Lincoln Stein 12:36, 17 April 2007 (EDT)