This is great news, thanks for letting us know.
--nate
On Oct 22, 2013, at 2:34 PM, Elwood Linney wrote:
thank you all, its clearly working now and that is coming just in
time, the results of two of these datasets will help us plan our next experiments for
capping up a manuscript or two
el linney
On Tue, Oct 22, 2013 at 12:03 PM, Nate Coraor <nate(a)bx.psu.edu> wrote:
Hi Elwood,
Jeremy and I took at a look at this. The failures in your history with this message:
Error: number of labels must match number of conditions
...are due to a regression in the cuffdiff tool which Jeremy has just fixed. Some
characters such as spaces in the condition name were valid prior to the move, but after
the move they became invalid. They should now be valid once again.
You've got one tophat job running and a cuffdiff job queued, and the rest of your
grey datasets are waiting for those two jobs to be finished before they'll be queued
(we'll be working on creating a visual distinction for this). I fixed the queued
cuffdiff job, which I believe should allow it to run without error (or at least, not the
same error).
--nate
On Oct 22, 2013, at 9:56 AM, Jennifer Jackson wrote:
> Elwood,
>
> Would you please share:
>
> 1. an original history that worked (if possible)
> 2. the workflow you are using and let me know how you generated (did you extract it
recently (last week or so)?
> 3. problem history
>
> There are a few known issues in here, some mitigated, one that has to do with
extracted workflows from existing older histories that is Cuffdiff specific (actually, a
few problems, found another last night). I want to rule those out or at least try to
provide feedback.
>
> I am at a conference over next several days, so let's use galaxy-bugs as a cc
whenever we communicate so nothing is left lingering, plus I know Nate was looking into
some of your data. Jeremy may jump also in at any time and help - he is the author of the
wrapper.
>
> So, in your reply, remove galaxy-user(a)bx.psu.edu and add galaxy-bugs(a)bx.psu.edu
>
> Jen
> Galaxy team
>
> On 10/22/13 5:42 AM, Elwood Linney wrote:
>>
>> After successfully using RNAseq software in Galaxy online for about 10
different datasets to just get gene expression differences between replicates from control
versus exposed zebrafish embryos, I am having no luck getting cuffdiff to work with the
"moved" Galaxy.
>>
>> I had this problem with histories developed before the move and histories
developed after the move.
>>
>> I have had this problem using an order cuffmerge gtf file that worked in the
past in Cuffdiff, with a new cuffmerge file developed from cufflinks of the files and by
just using a ref file gtf from UCSC.
>>
>> I don't know if this is just some interface problem with a different version
of the software that was included with the move, or a reference genome that does not
interface with Cuffdiff. It has happened with about 5 different histories.
>>
>> Is anyone else having this problem? And found a solution?
>>
>> Elwood Linney
>>
>>
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> --
> Jennifer Hillman-Jackson
>
>
http://galaxyproject.org
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
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> at
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> using "reply all" in your mail client. For discussion of
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>
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> To manage your subscriptions to this and other Galaxy lists,
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>
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