Perhaps you could set up a 64-bit Ubuntu repository to facilitate installation locally?
Mike Chelen commented
BioLinux itself has a repository, see: http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/package-repository
Steffen Möller commented
A compatibility would indeed be great. Debian + Ubuntu do have quite a vibrant bioinfo community that you can contact via http://debian-med.alioth.debian.org. Missing tools are fairly easily added, please send your requests to the mailing list. The major challenge as it seems is the integration with data, and the contribution from the JCVI and you all is much appreciated to get there.