Bio-Linux - Bioinformatics Tools for Linux

March 07, 2008

Bio-Linux is a specialised Linux disro that provides both standard and cutting edge bioinformatics software tools on a Linux base.

I wrote a post on my old blog a little while back now detailing how to use the packages from Bio-Linux in Ubuntu Linux, but it got missed in the migration (sorry to all those who have been searching for it). Here’s a repost and update for Ubuntu 7.10…

Log into your system and open up a terminal, then follow these steps:

sudo gedit /etc/apt/sources.list

Add the following lines to the end of the file:

# Bio-Linux package repository
deb http://envgen.nox.ac.uk/bio-linux/ unstable bio-linux

Save and close the file, now back at the terminal type the following (Note that we need to install the bio-linux-staden package, without this we’d have to do a bit more hacking in config files to stop getting errors whenever we open up a terminal):

sudo apt-get update
sudo apt-get install bio-linux-base-directories bio-linux-staden

Next step is to set-up your environment for Bio-Linux…

sudo gedit /etc/bash.bashrc

Add the following lines to the end of the file:

# Set up Bio-Linux Environment
source /usr/local/bioinf/config_files/aliasrc
source /usr/local/bioinf/config_files/bioenvrc

Save and close the file.

That’s it, now all of the packages available through Bio-Linux are now available to you in Ubuntu. One final word of warning… I’ve noticed that a few of the packages are a little out of date, (the Bio-Linux version of Taverna is 1.4, but 1.7 is now available) so it might be worth checking the version numbers before installing things.

The other thing to note with the Bio-Linux version of Taverna - it doesn’t start properly without a little bit of hacking… :( (If you decided to go with the Bio-Linux version, you can launch it by running the following in the terminal: /usr/local/bioinf/taverna/taverna/runme.sh).