Add versioning to the GTF file by recording the original file path.
Add versioning to the GTF file by recording the original file path.

Refactor of this script so it will work with a user-supplied
genomic FASTA file and GTF file, to decouple it from a bcbio-nextgen
installation.

rchekaluk/cloudbiolinux,elkingtonmcb/cloudbiolinux,rchekaluk/cloudbiolinux,pjotrp/cloudbiolinux,pjotrp/cloudbiolinux,joemphilips/cloudbiolinux,joemphilips/cloudbiolinux,pjotrp/cloudbiolinux,elkingtonmcb/cloudbiolinux,joemphilips/cloudbiolinux,AICIDNN/cloudbiolinux,chapmanb/cloudbiolinux,chapmanb/cloudbiolinux,AICIDNN/cloudbiolinux,chapmanb/cloudbiolinux,rchekaluk/cloudbiolinux,AICIDNN/cloudbiolinux,chapmanb/cloudbiolinux,elkingtonmcb/cloudbiolinux,AICIDNN/cloudbiolinux,elkingtonmcb/cloudbiolinux,rchekaluk/cloudbiolinux,pjotrp/cloudbiolinux,joemphilips/cloudbiolinux