Latest VirtualBox on Ubunut 12.04 DNS stopped working.  See http://serverfault.com/questions/453185/vagrant-virtualbox-dns-10-0-2-3-not-working
Merge remote-tracking branch 'origin/feature/brian_pancan_fixes' into feature/brian_pancan_fixes

Conflicts:
	templates/Vagrantfile_part.template
Adding in deps for a pancan workflow
Fixes for SGE: making memory consumable, setting correct number of slots
Adding a md file that will eventually be migrated to the PanCan wiki space.  Keeping this close to the code until it's ready
Configure -pe serial for SGE
Download HelloWorld from S3 and install the bundle
Fix SGE parallel environment settings

The desired behaviour is for all nodes of parallel jobs to be on the same machine.
This requires the strategy $pe_slots, not $fill_up as it was set before. The total number of nodes has also been set to 9999 so that it is limited by the actual nodes available on each machine.
Fix for incorrect install command in seqware master install script
Adding  some docs, adding vagrant user script primarily intended for VirtualBox workflow development
Adding templates so pancancer tools are seperate
Fixing the default value
Fixing small problem with seqware bin for vagrant user
Merge remote-tracking branch 'origin/feature/brian_pancan_fixes' into feature/brian_pancan_fixes
Updating the README for the 1.1 release.
Working on the README
Adding BWA workflow profiles for PanCancer, updating readme
Working on the readme
Working on templates
Adding pancancer setup script