Bioinformatics and Debian-associated repositories

Bio-Linux Bioinformatics package repository

The Bio-Linux Bioinformatics package repository contains the Bio-Linux 4 bioinformatics software and can be installed from a centralised repository located on the EGTDC server. The packages available from this site have been created by the EGTDC specifically for the Bio-Linux project and are in deb format.

The projects claim to be compatible with any installation of Debian or Debian variants. This might be a weak sentence because Debian variants are quite different. It is better to say exactly Debian "stable" or Debian "testing" and draw a line between native Debian and perhaps commercial derivatives which might differ in certain aspects.

The packages are not, however, core Debian packages. Please read the notes below for further details about Bio-Linux packages. They add the following notes:

  1. All of the packages have a dependency on the package bio-linux-base-directories, as this is the package that sets up the directory structure and dependencies of several of the Bio-Linux system packages. This creates a number of directories and configuration files for Bio-Linux but will NOT overwrite anything on your system. Therefore you may wish to install this package first, or force the install of other packages if you do not want to install this package.
  2. Warning: The bio-linux-bldp-files package contains files which install to a folder called /var/www/boinformatics. Thus, please ensure that you do not already have a directory on your system of this name, or that, at the very least, you are not concerned with overwriting any index.html file in such an existing directory.
  3. All packages install to /usr/local/bioinf and create symlinks in /usr/local/bin with the exception of the bio-linux-genespring software which installs to /home/db/SiliconGenetics (for more information regarding installation of GeneSpring, see our GeneSpring Web Page.)
  4. Bio-linux-base-directories installs two files into /usr/local/bioinf/config_files (bioenvrc and aliasrc). The file bioenvrc should be sourced by your shell if you want to pick up the correct environmental variables for the software. We recommend the use of the z-shell for Bio-Linux. You will also want to source aliasrc if you wish to run some of the Java based software - for example maxdView, maxdLoad2, mesquite, forester, etc. You will also need to edit the aliasrc file to reflect the location of the Java binaries on your system.

The authors did a great job in collecting a certain amount of very useful software for biologists and the Debian-Med project might try to include some packages which are not yet available in Debian officially.

BioLinux-BR Project

A similar project is the BioLinux-BR Project which is a project directed to the scientific community. Their goal is to create a Linux distribution for people with little familiarity with the installation of the operational system and mainly for people who do not know to proceed unpacking a program, compile and install it correctly.

For these reasons, they want to give contribution, developing a Linux system that aims to be easy to use and still offering packages that will be part of the BioLinux-BR. Giving this option, we will not be compelling anybody to change its Linux distribution, since there are packages developed for the greater Linux distributions.

"BR" here stands for "Brasil" which might lead to the assumption that some internationalisation effort was done, but according to the authors this was not their main concern but rather a side effect.

In fact, this project has assembled a huge amount of packages, probably the most complete collection of Free Software in biology. Packages for multiple distributions are provided, which includes Debian, and a live CD.

Debian developer Matt Hope has created a small set of packages for Debian that he has not yet uploaded to the main distribution. Most are in a very nice state he just should submit.

Andreas Tille 2005-05-13