Difference between revisions of "GBrowse RPM HOWTO"
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RPM-based Linux distributions, including [http://fedoraproject.org/wiki/ Fedora Core] and [http://www.centos.org CentOS], can install GBrowse using the RPMs located at http://www.biopackages.net/. These can be installed using the [http://en.wikipedia.org/wiki/Yellow_dog_Updater_Modified yum] installer tool. | RPM-based Linux distributions, including [http://fedoraproject.org/wiki/ Fedora Core] and [http://www.centos.org CentOS], can install GBrowse using the RPMs located at http://www.biopackages.net/. These can be installed using the [http://en.wikipedia.org/wiki/Yellow_dog_Updater_Modified 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 [http://biopackages.net] website. | + | 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 [http://biopackages.net] website. The platform tested for the GMOD community is CentOS 4 and we highly recommend using Biopackages on this distribution. |
=Preliminaries= | =Preliminaries= | ||
Revision as of 19:05, 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 [1] website. The platform tested for the GMOD community is CentOS 4 and we highly recommend using Biopackages on this distribution.
Preliminaries
To configure yum to be aware of the Biopackages.net repository, add the following to your /etc/yum.conf file:
[biopackages-stable] name=BioPackages (Stable) for Fedora Core $releasever - $basearch baseurl=http://yum.biopackages.net/biopackages/stable/fedora/$releasever/$basearch/
[biopackages-stable-noarch] name=BioPackages (Stable) for Fedora Core $releasever - noarch baseurl=http://yum.biopackages.net/biopackages/stable/fedora/$releasever/noarch/
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: BioPackages (Testing x86_64) for Fedora Core 2 - x86_64 Server: BioPackages (Testing 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.
