Added creating a GTF file of all of the large exons.

This is useful for more accurate insert size calculations.
Handle identification of GATK version from install directory: works with protected and lite versions
Update to latest version of freebayes. Add clang to standard compilers
Retain the created GTF dbs.
Merge branch 'master' of https://github.com/chapmanb/cloudbiolinux
Handle setting user level access for share/java for homebrew installs of java programs. Thanks to @heuermh
Add GRCh37.
Merge branch 'master' of github.com:chapmanb/cloudbiolinux