Although the courses we teach do not require that students to know how to program, we strongly advise them to get their acts together and learn at least one programming language. In addition, some minimal components are require to compile bioinformatics applications from source code. For Impilo, I decided to install the necessary tools to exploit the three most used toolboxes in bioinformatics: BioPerl, BioPython and BioJava.

Since we created the basic virtual machine using the LAMP Server option, minimal installs for Perl, PHP and Python already exist in Impilo. The file named develop_module.txt has the list of all supplementary packages needed and installed from Ubuntu repository. As always, its content will evolve according to Ubuntu's decisions and users' feedbacks.

WARNING! Ubuntu has chosen to not include Sun's JDK 6 in its readily accessible packages. It is very easy to change this thanks to these commands:

% add-apt-repository "deb http://archive.canonical.com/ lucid partner" && sudo apt-get update

Why not use OpenJDK? Simply because some applications that we are including just don't work properly with it…

In the case of Biojava, since no package per se does exist for it, I took some liberties. I installed the latest stable release and put the JAR files inside the external library folder in Ubuntu: /usr/lib/jvm/java-6-sun-1.6.0.<number>/jre/lib/ext. Since this is in the default CLASSPATH, the libraries can than be used by any user, for any program.