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Biopackages HOWTO

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Biopackages

RPM-based Linux distributions, including Fedora Core and CentOS, can install GMOD software (chado databases, GBrowse, GMODWeb, etc) using the RPMs located at http://www.biopackages.net/. These can be installed using the yum installer tool. This process is an easy and quick way to install GMOD tools. The only requirement is that you use one of the supported distributions (Centos4 is the supported & tested platform for GMOD) and you install biopackages on a clean system (e.g. no source installed software). We recommend you do not mix source and RPM software installs unless you really know what you are doing since they could (silently) conflict with each other. See the section "Source vs. RPM Installs" below for more information.

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, you can view the build status for our RPMs here. 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)

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:

rpm -Uvh http://biopackages.net/biopackages/stable/centos/4/noarch/biopackages-client-config-1.0-1.2.bp.centos4.noarch.rpm

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

You can then install any RPM package available through Biopackages. For a list of RPMs please see the build status report. You can also browse the repository directly here.

There are many GMOD RPMs available including:

  • chado, chado-Sce, chado-Hsa, chado-Mmu (base empty chado with ontologies, chado for yeast, chado for human, chado for mouse respectively)
  • gmod-web, gmod-web-Sce, gmod-web-Hsa (GMODWeb pre-configured)
  • gbrowse
  • textpresso
  • AmiGO
  • blastGraphic
  • turnkey
  • R
  • bioperl
  • ncbi (the NCBI toolkit)
  • and many others

Use the following command as root to install one, or more, of these packages:

% yum install <package_name>

Help! Package Foo on Platform X Does Not Work/Is Not Available

Since the biopackages project is a relatively small group of developers we are currently focused on Centos4. If you encounter bugs on this, or another, platform we would like to hear about them. Please email the Biopackages [list] a detailed bug report.

If the package you are interested in is not available or is out-of-date please consider becoming a Biopackages developer. More information can be found on our developers wiki at http://biopackages.wiki.sourceforge.net.

Source vs. RPM Installs

Since RPMs and source installs can silently overwrite each other resulting in conflicts we recommend you do not mix them. If you must install source, for example to support software development, we recommend you specify the source installation directory to be either 1) a specific development directory in you home directory or 2) a non-standard system folder such as /usr/local. This way your core operating system will be maintained as a clean, RPM-only environment.

Authors

Brian O'Connor