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 

From: Jeremy Goecks [mailto:jeremy.goe...@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 

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 


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?


Attachment: gtf_indices.loc
Description: gtf_indices.loc

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