1.) Please see attached.

2.) So I did this for tophat and cufflinks. This would be useful for cuffcompare. Cuffdiff uses the gtf files output from cufflinks and not reference gtf files.

Following a conversation we had with James, I plan on editing the xml scripts to pull the genome attributes from a previous step as opposed to having to set them.

From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu]
Sent: Wednesday, October 12, 2011 1:22 PM
To: Chorny, Ilya
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: Some changes to tophat and cufflinks wrappers for indexing loc files

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.