Are you reporting a bug for each failed Cuffdiff run? That's the easiest way 
for the Galaxy team to help you out. One thing to keep in mind is that, for 
now, spaces are not allowed in condition names. We'll address this problem soon.

Best,
J.



On Oct 22, 2013, at 5:42 AM, Elwood Linney <ellin...@gmail.com> 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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