Jeremy, Do you guys have an ETA for launching the data table changes? Thanks, Ilya From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu] Sent: Monday, October 03, 2011 5:41 AM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: Some changes to tophat and cufflinks wrappers for indexing loc files Thanks Ilya. This is definitely something we plan to include in Galaxy, but I'd been holding off looking into it because of the our planned changes to the tool data tables. Once these enhancements are in place, I'll take a look at these patches and ensure that they are compatible with these changes. Best, J. On Sep 30, 2011, at 6:20 PM, Chorny, Ilya wrote: 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<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com/> <cufflinks_wrapper.xml.diff><tophat_wrapper.xml.diff>

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.