Update bcbio conda build to support latest bcbio-nextgen-vm. Clean up Dockerfile
Bug fix for correctly grouping multi-caller/multi-batch variant calls
Joint squaring off: add initial integration with bcbio-nextgen-recall, needs additional work to handle regional calling
Easier prep for custom genomes.

This hooks until the cloudbiolinux preparation stuff and is
super hacky but as a place to get started making this a little bit
easier.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Remove development code.
Merge pull request #448 from kern3020/master

enable sacCer2, update urls and fixes some typos
Joint/batch calling: Merge regional batches into single final batch. Correctly reconstitute orignal variation files if calling and joint calling both done. Feed joint callers into gemini database creation instead of initial calls
Fix joint calling test data to use correct ploidy and have additional reference call tests
Integrate LOFTEE VEP plugin from @konradjk to support annotating predicted loss of function variations
pass extra args (for example, --pdb) to the testrunner
Merge pull request #450 from jwm/testrunner_passthrough_extra_args

pass extra args (for example, --pdb) to the testrunner
fix for #451