Updating vcr.py: Installs viral assembly and viral VIGOR
Modified to match new vcr.py (updated 2013-01-07)
Pulls vir-assembly-pipeline.sh from amazomaws repo in place of github
Adding argument env to all install functions for compatibility with fabfile.py
Merge pull request #58 from jmchilton/master

Implement mechanism to supply user data defaults to CloudMan.
Function _enable_galaxy_on_sudo() adds galaxy privilieges on /etc/sudoers
When configuring Galaxy, add tools/bin dir and stick it in PATH as a catch-all, custom tools location for users. Also so PEP8 cleanup
Merge branch 'master' of github.com:JCVI-Cloud/cloudbiolinux
Merge pull request #59 from JCVI-Cloud/master

Latest update of Viral Cloud Resource (VCR) tools from JCVI
Update bowtie2, tophat and cufflinks to latest versions
Add build target for bcbio.variation to support ensemble calling
Work on bringing proteomics tools into cloudbiolinux to configure cloudman/galaxy instances for protoemics.

This work includes setting up custom installs (for vanilla cloudbiolinux or Galaxy tool) for Transproteomic Pipeline (TPP) (including proteowizard and X! Tandem), OMSSA, Percolator, Fido, mzmine, the Tabb lab software (myrimatch, pepitome, tagrecon, and idpQonvert), iQuant, PepNovo, iPiG, PRIDE Inspector, and PRIDE Converter 2. Additional galaxy specific installs for Ira Cooke's protk toolkit and the protvis visualizer.
Implement framework for adding wine based applications packaged using this work - https://github.com/jmchilton/proteomics-wine-env.

Use this framework to implement installation code for the Proteowizard suite and multiplierz.