What's available?
Biopackages.net currently provides packages as RPMs for Fedora Core Linux, CentOS Linux, and Apple Darwin (OS X). Packages can be browsed and downloaded directly for both stable and testing repositories. These are also available by using yum. See Configuration for details on how to set up yum to be Biopackages-aware. Notable packages available include Bioperl, Bioconductor, The Generic Genome Browser, Chado, Turnkey, GMODWeb, Textpresso, BLAT, EMBOSS, and Hmmer.
Configuration
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:
Some of our packages depend on other packages that are maintained by RPMForge, so please also install the respective RPMForge configuration RPM: A simple way to do this is, as root, execute the following command. Make sure you substitute the URL below with the correct one for your distribution from the links above:rpm -Uvh http://biopackages.net/stable/centos/4/noarch/biopackages-client-config-1.0-1.5.bp.centos4.noarch.rpm
/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/ [rpmforge] name = RPMforge.net for CentOS $releasever - dag baseurl = http://apt.sw.be/redhat/el4/en/$basearch/dag enabled = 1 gpgkey = file:///etc/pki/rpm-gpg/RPM-GPG-KEY-rpmforge-dag gpgcheck = 1
/etc/pki/rpm-gpg.
Finding Packages
See the "provides" and "search" sections of the yum manpage.
Visit the report page to see the build progress in the testing repository (which are periodically published in the stable repository).
Testing packages are available here but undergo frequent revision and yum may fail to download these properly since the yum metadata is only updated periodically.
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
% yum install perl-bioperl yum install chado-Sce Gathering header information file(s) from server(s) Server: BioPackages (Stable) for Fedora Core 2 - i386 Server: BioPackages (Stable) for Fedora Core 2 - noarch Server: BioPackages (Testing) for Fedora Core 2 - i386 Server: BioPackages (Testing) for Fedora Core 2 - noarch Server: Fedora Linux 2 - i386 - updates Finding updated packages Downloading needed headers biopackages-0-1.0.0-6.noa 100% |=========================| 1.7 kB 00:00 usr-local-bin-perl-0-1.0- 100% |=========================| 833 B 00:00 Resolving dependencies Dependencies resolved I will do the following: [install: perl-bioperl 1.5-8.cvs20050328.bp.fc2.i386] Is this ok [y/N]: y Downloading Packages Running test transaction: Test transaction complete, Success! perl-bioperl 100 % done 1/1 Installed: perl-bioperl 1.5-8.cvs20050328.bp.fc2.i386 Transaction(s) Complete
How can I Contribute?
We hope to provide packages for these other system/package manager combinations in the near future:
If you're already a packager, or just willing to learn, and are interested in contributing, porting and/or maintaining packages with biopackages.net, please email the Biopackages mailing list. Also take a look at the Biopackages developers site on SourceForge and our developers documentation wiki. The developer quickstart guide is a good place to begin.Other Useful Package Repositories
