Additional work towards supporting runs using docker containers: merge host and container system configurations and remap galaxy loc directories. Provide a testing server approach to allow in-docker updates and testing of changes
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Remove ipdb call.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Re-enable --quiet for Cufflinks.