> The problem ended being the use of "Perform Bias Correction"(-b) and a
> GTF file with no "Database/Build" associated. Looking at cuffdiff
> wrapper I found, if a FASTA reference is not selected from the
> history, the FASTA reference of the GTF file associated build is used.
> If there is not build association, your cuffdiff run will fail with
> this not so helpful error.
> My feeling is, cuffdiff should check for a non-dashed string after
> '-b' and complain if is absents, but this doesn't happen currently.

Agreed. I implemented the spirit of this functionality via argument checking in 
galaxy-central changeset 71031bf3105c

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