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
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.
Explicitly list samtools binaries to install. find command failed on OSX. Thanks to @udp3f
Add packages needed for protk RVM install.
Proteomics: Add more debconf selections for Galaxy-P. Automated install still not quite there, asked to configure GDM and mail server?.
Allow building fresh CloudMan instances from scratch using the CloudBioLinux deployer - including what I believe is the first available documentation for how to do this (using any method). All updated for latest CloudMan changes (merged tools&volumes), reworked snaps.yaml configuration, etc....
Deployer: Add action for bundling a local copy of CloudMan and dropping it in bucket_source.
Remove files accidently added during a previously commit that shouldn't have been.
Galaxy: Add -f to ln calls at the end of _configure_galaxy_repository so the procedure can be recalled on existing repository.
Deployer: Add some quick documentation to cloudman.md about how to customize tools, galaxy, cloudman (presumably if someone is building a CloudMan image they will want to do one of these).