Internally we have installed the x64 version of the latest Ubuntu distribution - named 8.04. You can choose either Ubuntu for GNOME or Kubuntu for the KDE desktop environment, it does not matter to the SNP & Variation Suite, it's just a personal preference. We use Kubuntu. The key is to get the 64 bit version (sometimes called amd64 but it's not AMD or Intel specific).
Once installed, you must install the 32-bit compatibility libraries and the Sun Java JRE. You get these in a console by running sudo apt-get install ia32-libs sun-java6-jre and SVS will run fine, but remember it's limited by it's 32-bit address space of 4GB of RAM.
