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
Update Hadoop download files; update several doc strings
Use minimal edition as target to avoid doing whole system upgrades or touching package lists
Cleanups to handle minimal install of specific flavors, specifically targeting installation of bcbio-nextgen pipeline tools