Update bwa to the latest release
Update bwa to latest release
Update gemini installation to use standard installer. Bump bcbio.variation to latest release
A BOSC reviewer helpfully noted that while the README contains reference to the license, it is good practice to actually distribute the license with the code.
Merge pull request #72 from jmchilton/master

Add LICENSE.txt file
License to cloudbiolinux contributors
Bug fix related passing arguments from fabric to puppet classes.
Allow install procedure to differ from galaxy requirement name (e.g. install_blast sets up a blast+ requirement file).
Proteomics: Rev tint scripts install version.
Rev version of biocloudcentral puppet module to target.
Work toward creation of a flavor to setting up an open source version of swift, an open source proteomics web application for combining multiple proteomic search engines.

For more information on swift see:
- https://github.com/romanzenka/swift
- http://informatics.mayo.edu/svn/trunk/mprc/swift/index.html).
Proteomics: Update proteowizard download URL. Really need to setup a stable download location.
Add custom package repo for HTCondor (HTCondor package for Ubuntu 12.04 is available there)
Proteomics: New custom install method for crux. Update software versions of PeptideShaker and SearchGUI, small cleanups of other custom method.
Merge branch 'master' of https://github.com/chapmanb/cloudbiolinux
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