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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