Update freebayes to latest revision with fixes for soft-clipped reads at start of contigs
Remove RVM install from ports on Ubuntu thanks to feedback from @jmchilton
Proteomics: SearchGUI/PeptideShaker enhancements.
Implement new fabricrc option `autoload_galaxy_tools`. This defaults to False, but if True it will cause the sourcing of galaxy env.sh to be placed into `user`'s .bashrc file. This allows galaxy to maintain separate isolated environments, while also letting users easily utilize tools setup for Galaxy from the command-line. This should be considered a highly experimental feature, it has clear problems (potentially loading conflicting virtualenv environments for instance).
libtokyocabinet9 is not available in Ubuntu percise, but libtokyocabinet-dev brings in libtokyocabinet8. So I think a more generic way to get this library is just install the dev package (as done with the following line).
Add R libraries for mass spec analysis, along with required system library (libnetcdf-dev) required by one of these packages. Mostly these libraries are the ones outlined by @ypriverol in this blog post http://www.r-bloggers.com/why-r-for-mass-spectrometrist-and-computational-proteomics/.
Proteomics: Clean up and updates for MZMine, OpenMS, PeptideShaker, SearchGUI, and pride tools.
Proteomics: Work toward building a flavor for combined Galaxy + CLI + Desktop usage modeled after the awesome Current Protocols papers. Adding R & Ruby libraries to galaxyp flavor.