Handle missing download directories on non-ubuntu filesystems
Latest Picard version
Build for Plink/Seq
Merge branch 'master' of github.com:chapmanb/cloudbiolinux
Make RabbitMQ installation non-interactive; thanks to @aryantaheri
Handle oneiric specific packages; thanks to @aryantaheri
Install python3 packages; thanks to @aryantaheri
Install instructions for Bio4j; thanks to Pablo Pareja
Update R mirrors; thanks to @aryantaheri
Avoid zero length field names in format which only work on 2.7; thanks to @aryantaheri
Added unknown (non-sequenced or assembled) genomes
Additional next-gen software: last-align, ECHO, dwgsim, stampy, CRISP. Thanks to Ross Whetten for suggestions
Update TopHat and Cufflinks versions
Custom builds for TASSEL and STACKS; thanks to Ross Whetten
Add links to configuration files; thanks to Ross Whetten
Python libraries: pybedtools and PyVCF
sqlite3-ruby is renamed to sqlite3
Fixing Lucid  rubygem dependencies
Merge
A comment about flowsim, failing on Lucid