4:03 p.m.
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
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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