Proteomics: Bug fix for crux install method. Rev PeptideShaker and SearchGUI again.
Proteomics: Add peptide_to_gff (https://bitbucket.org/galaxyp/peptide_to_gff) tool written by Jim Johnson to bio_proteomics.
Add custom install procedure for kent_tools (blat).

I guess there are potential some license issues with this, but it will not be automatically installed in the official CloudBioLinux image so I hope this is not a problem. Let me know if this is not the case however.
Proteomics: Cleanup wine stuff and install procedure for Morpheus. http://www.chem.wisc.edu/~coon/Downloads/Morpheus/
Proteomics: Revert to version 4.6.1 of the trans proteomic pipeline (at least by default), 4.6.2 has bugs making it incompatible with ProtK. Reported bugs here: https://groups.google.com/forum/\?fromgroups#discuss/a9LF_Y_NU_M
Proteomics: Update ProtK install procedure to reflect Galaxy tool for Blast is not called blast+ to bring inline with actual wrappers.
Galaxy: This is a little questionable, anyone should feel free to redo this or undo this if it breaks anything. The problem is that the latest version of python-rpy targets R 3.0.0, but the latest r-base (the one that gets installed is 3.0.1) so python-rpy doesn't work and Galaxy tools break.