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Difference between revisions of "GBrowse RPM HOWTO"
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=Preliminaries= | =Preliminaries= | ||
− | To configure yum to be aware of the Biopackages.net repository, add the following to your /etc/yum.conf file: | + | 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: |
+ | |||
+ | * [http://biopackages.net/biopackages/stable/fedora/2/noarch/biopackages-client-config-1.0-1.2.bp.fc2.noarch.rpm Fedora Core 2] | ||
+ | * [http://biopackages.net/biopackages/stable/fedora/5/noarch/biopackages-client-config-1.0-1.2.bp.fc5.noarch.rpm Fedora Core 5] | ||
+ | * [http://biopackages.net/biopackages/stable/centos/4/noarch/biopackages-client-config-1.0-1.2.bp.centos4.noarch.rpm CentOS 4] (the recommended Linux distribution) | ||
+ | |||
+ | Alternatively you can manually add the following to your /etc/yum.conf file (customize as appropriate): | ||
[biopackages-stable] | [biopackages-stable] | ||
name=BioPackages (Stable) for Fedora Core $releasever - $basearch | 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/$basearch/ | baseurl=http://yum.biopackages.net/biopackages/stable/fedora/$releasever/$basearch/ | ||
− | + | ||
[biopackages-stable-noarch] | [biopackages-stable-noarch] | ||
name=BioPackages (Stable) for Fedora Core $releasever - 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/ | baseurl=http://yum.biopackages.net/biopackages/stable/fedora/$releasever/noarch/ | ||
+ | |||
+ | And import the public key from [http://biopackages.net/BIOPACKAGES-RPM-GPG-KEY here], saving it to /etc/pki/rpm-gpg. | ||
=Installing Packages= | =Installing Packages= |
Revision as of 19:10, 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
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: 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.