Add ability to pass a custom GTF file.
Add ability to pass a custom GTF file.

This removes the restriction of relying on Ensembl/UCSC annotations.

AICIDNN/cloudbiolinux,lpantano/cloudbiolinux,heuermh/cloudbiolinux,rchekaluk/cloudbiolinux,kdaily/cloudbiolinux,lpantano/cloudbiolinux,kdaily/cloudbiolinux,AICIDNN/cloudbiolinux,joemphilips/cloudbiolinux,chapmanb/cloudbiolinux,pjotrp/cloudbiolinux,averagehat/cloudbiolinux,chapmanb/cloudbiolinux,AICIDNN/cloudbiolinux,chapmanb/cloudbiolinux,heuermh/cloudbiolinux,pjotrp/cloudbiolinux,chapmanb/cloudbiolinux,AICIDNN/cloudbiolinux,elkingtonmcb/cloudbiolinux,joemphilips/cloudbiolinux,elkingtonmcb/cloudbiolinux,joemphilips/cloudbiolinux,rchekaluk/cloudbiolinux,pjotrp/cloudbiolinux,joemphilips/cloudbiolinux,averagehat/cloudbiolinux,heuermh/cloudbiolinux,pjotrp/cloudbiolinux,heuermh/cloudbiolinux,lpantano/cloudbiolinux,kdaily/cloudbiolinux,averagehat/cloudbiolinux,kdaily/cloudbiolinux,rchekaluk/cloudbiolinux,elkingtonmcb/cloudbiolinux,elkingtonmcb/cloudbiolinux,rchekaluk/cloudbiolinux,averagehat/cloudbiolinux