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