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).
Deployer: Update sample galaxy_home to /mnt/galaxy/galaxy-app. It seems to be supported and it is a little more generic. Also change example galaxy-p example URL to not use the cloud modified version, it does not work with this setup.
Further enhancements to CloudMan documentation. Rework galaxyp flavor into two flavors and server and desktop version. Add some actual documentation for Galaxy-P.
Proteomics: Add missing gnuplot dependency required by TPP.