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 attri
> 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 co
Jeremy,
Do you guys have an ETA for launching the data table changes?
Thanks,
Ilya
From: Jeremy Goecks [mailto:jeremy.goe...@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
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 chan
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 Sci
