Add STAR indexing.
Add STAR indexing.

Small refactor to change the order of things. Download
the transcripts first and then create the indexes after.
This lets indexers that need a GTF file to be created.

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