I made some changes to the cufflinks and tophat wrapper to pull gtf files from an indexed loc file as  opposed to from history. The diff’s are attached. I made it an optional feature. Please let me know if this makes its way into galaxy-central.

Ilya,

This looks like a good start. A couple questions:

(1) Do you have a sample GTF indices file similar to e.g. bowtie_indices.loc.sample ?
(2) Would it be useful to provide GTF index files in Cuffcompare, Cuffdiff, and Tophat as well?

Thanks,
J.