Update version detection to include all recently added third party tools. Utilize brew which to retrieve versions of tools installed via brew method.
Output genome resource data into the project summary file.

This way downstream tools can parse it to figure out what was
used.
More verbose project-summary output.
Command line improvements: provide useful errors for incorrect ipython/scheduler/queue args. Fixes #205. Provide useful help message for upgrade with no inputs. Increase allowed resource usage within available hard limits. Fixes #214
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen