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.

Best,

Ilya

Ilya Chorny Ph.D.

Bioinformatics Scientist I

Illumina, Inc.

9885 Towne Centre Drive

San Diego, CA 92121

Work: 858.202.4582

Email: ichorny@illumina.com

Website: www.illumina.com