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
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.
Fusion of what was the galaxy-vm-launcher into CloudBioLinux. The galaxy-vm-launcher was an alternative method for building and launching Galaxy cloud images to the mi-deployment/CloudMan workflow. The galaxy-vm-launcher is used at the University of Minnesota as the launching point for a CLIA-certified Galaxy-based variant detection workflow.

As I helped migrate mi-deployment into CloudBioLinux, I made numerous modifications to allow reuse between the CloudMan setup code and the fucntionality in this changeset. This changeset isn't just moving galaxy-vm-launcher into the same repository as CloudBioLinux, this code base has been heavily modified to make use existing code in CloudBioLinux and vise versa.

While this mechanism for building Galaxy images does not result in all of the bells and whistles available via CloudMan (auto-scaling, admin console, FTP server, share-strings), it does allow a user to launch and clean Ubuntu image, configure it with CloudBioLinux+Galaxy, and transfer data to the VM and into a Galaxy data library all from a single command-line execution and configuration file. This gives rise to easy, automated multi-cloud reproducibility and could provide a path to real hybrid cloud computing.

As part of the migration several enhancements to this code were made, these include:
 - Added some initial CloudBioLinux and CloudMan support. Actions for install CloudBioLinux and launching packaged CloudMan instances have been added. Added ability to tweak CloudBioLinux fabricrc commands, specify CloudBioLinux flavor, and set CloudMan user data from unified settings.yaml file.
 - Refactored the code to provide uniform access to options (be they coming from command-line arguments or a YAML settings file.).
 - Moved all command-line argument and yaml parsing logic into its own small file - main.py. This files simply builds up a python dictionary and passes that to the deploy function in cloudbio.deploy. The upshot of this is that the python dictionary could be built up in some other fashion (perhaps by a webui such BioCloudCentral of Refinery for instance)  and all of the functionality can utilized as a python library.
 - Input settings file can now be specified at runtime (deploy.sh --settings=/path/to/settings.yaml).
 - As part of synchronizing properties between CloudBioLinux and galaxy-vm-launcher, many new paths and settings were parmaterized and can now be overridden if needed.
 - Implemented automated packaging of of instances for OpenStack.
 - Support for versions of Ubuntu prior to Ubuntu 12.04 LTS was dropped.