> 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.


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?


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