GBrowse RPM HOWTO

From GMOD

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1 Important note
2 Biopackages
3 Preliminaries
4 Installing Packages
5 Authors

[edit] Important note

These directions will install a relatively old version of GBrowse (1.54 I think). To install a newer version, install the Apache webserver (httpd) and libgd with yum:

 sudo yum install gd-devel httpd

and then follow the directions on the main install page for using the net install script.

[edit] Biopackages

RPM-based Linux distributions, including Fedora Core and CentOS, can install GBrowse using the RPMs located at http://www.biopackages.net/. These can be installed using the yum installer tool. For more information please see the Biopackages HOWTO.

[edit] Preliminaries

See the Biopackages HOWTO for the steps to setup Biopackages on your system.

[edit] Installing Packages

First, as root, freshen your local cache of yum header files. Yum will print something similar to what is below:

% yum update
Gathering header information file(s) from server(s)
Server: Fedora Core 2 - x86_64 - Base
Server: BioPackages (Stable x86_64) for Fedora Core 2 - x86_64
Server: BioPackages (Stable noarch) for Fedora Core 2 - x86_64
Server: Fedora Core 2 - x86_64 - Released Updates
Finding updated packages
Downloading needed headers
genome-Sce-annotation-gen 100% |=========================| 1.1 kB    00:00     
genome-Sce-nib-0-S228C-3. 100% |=========================| 1.7 kB    00:00     
chado-Sce-0-S228C.0.003-2 100% |=========================| 2.0 kB    00:00     
genome-Sce-annotation-aff 100% |=========================| 1.2 kB    00:00     
genome-Sce-0-S228C-3.2005 100% |=========================| 1.7 kB    00:00

Then install gbrowse:

% yum install gbrowse

You can now visit the documentation and try out the example Yeast database by visiting http://localhost/gbrowse

NOTE: One problem with the RPM install is it currently installs gbrowse into it's own directory (e.g. /var/www/cgi-bin/gbrowse/). This means that the yeast example referenced in http://localhost/gbrowse should actually point to http://localhost/cgi-bin/gbrowse/gbrowse/yeast_chr1.