The problem with cuffdiff should be fixed.  Still looking at the tophat 
failures.

Thanks for your patience, and for sticking with us as we iron this out.

--nate

On Oct 9, 2013, at 7:52 PM, Jennifer Jackson wrote:

> Hi Elwood,
> 
> As I emailed to your direct question, we are looking at your bug reports in 
> detail and will get back to you there. Thanks for submitting the problems 
> that way.
> 
> For anyone else reading, if you find problems right now on the upgraded 
> server, we are most definitely interested in learning about them. Please 
> submit bug reports for anything odd, even if it seems small, and put in the 
> comments additional observations if you have time.
> 
> We appreciate the feedback, and your patience, as always!
> 
> Jen
> Galaxy team
> 
> On 10/9/13 1:04 PM, Elwood Linney wrote:
>> 
>> Hello,  I have been waiting a few weeks to process some RNA seq datasets but 
>> woke up this morning with lots of               steps red.  I thought it 
>> just might be because of the movement of the system but I processed steps 
>> for some histories and everything has turned red.
>> 
>> I also noticed that online Galaxy now has RNAseq steps separated into two 
>> sections--does this have something to do with the problems?
>> 
>> el linney
>> Duke University Medical Center
>> 
>> 
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> 
> -- 
> Jennifer Hillman-Jackson
> 
> http://galaxyproject.org
> ___________________________________________________________
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___________________________________________________________
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