Remove unused query-name sorting.

Thanks to @porterjamesj for the code-pruning, this is from his
pull request.
Removed unused module.
Generalize snpEff: now handle both brew installed ( bashrc wrapper) and original jar installations. Install databases inside genome data instead of at installation time. Enables support for lighterweight installs in docker and additional genome support.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen