Update bwa to the latest release
Add the ability to download len files required by Galaxy Trackster
When installing Galaxy, setup shed_tools dir (due to circular dependencies, could not reuse the same functionality in deploy module)
For S3 upload, check for presence of up to date files in S3 and skip upload if found. Thanks to Flix Johns for the suggestion
Merge
Updated versions of RNA-seq and fastq assessment software. Thanks to Glen Otero
Update VarScan to latest version
Avoid non-essential CloudBioLinux custom packages that require isolated Python environment for non-sudo installations. Fixes chapmanb/bcbio-nextgen#18
Avoid using tar --pax-option command unless explicitly needed to be more cross compatible with Mac OSX tar. Thanks to @udp3f
fix selecting flavor due to os.path.split and __import__ using filepath.
Merge pull request #75 from Traksewt/master

Fix flavor selection
use https:// protocol instead of git:// for git clone, allows for installation in environments where the git protocol is blocked by firewall rules
Merge pull request #76 from heuermh/master

Use https:// protocol instead of git:// for git clone
Update bio_nextgen.py

Prefer latest version of LUMPY: multiple bug fixes; this version is the basis of the journal subscription.
Merge pull request #77 from arq5x/master

Update LUMPY to most recent, stable version.
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