Revision as of 19:13, 19 April 2007

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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.

At the time of this writing (April 2007) complete RPMs for Fedora Core 2, 5, and CentOS 4 are available, and supported architectures included 32- and 64-bit Intel platforms. Check back regularly for updates at the Biopackages website. The platform tested for the GMOD community is CentOS 4 and we highly recommend using Biopackages on this distribution.

Preliminaries

Biopackages.net hosts a yum repository for distribution of Linux packages. To configure yum to be aware of the Biopackages.net repository, install one of the following configuration RPMs:

   * Fedora Core 2
   * Fedora Core 5
   * CentOS 4 (the recommended Linux distribution)

Alternatively you can manually add the following to your /etc/yum.conf file (customize as appropriate):

[biopackages-stable]
name=BioPackages (Stable) for Fedora Core $releasever - $basearch
enabled=1
gpgkey=file:///etc/pki/rpm-gpg/BIOPACKAGES-RPM-GPG-KEY
gpgcheck=1
baseurl=http://yum.biopackages.net/biopackages/stable/fedora/$releasever/$basearch/

[biopackages-stable-noarch]
name=BioPackages (Stable) for Fedora Core $releasever - noarch
enabled=1
gpgkey=file:///etc/pki/rpm-gpg/BIOPACKAGES-RPM-GPG-KEY
gpgcheck=1
baseurl=http://yum.biopackages.net/biopackages/stable/fedora/$releasever/noarch/

And import the public key from here, saving it to /etc/pki/rpm-gpg.

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

Authors

Lincoln Stein 12:51, 17 April 2007 (EDT)

Some material cut and paste from www.biopackages.net, with permission from Allen Day.

Brian O'Connor 12:12, 19 April 2007 (PDT)

Updated the install description of Biopackages to use our new configuration RPMs.