I ran into this error running cuffdiff. I had a hard time debugging
this user error, so I though it would be nice to share the solution.
This was in a local instance, but I don't see why it wouldn't happen
in Galaxy Main under the same circumstances.
Tool execution generated the following error message:
Error running cuffdiff. Error: cannot open reference GTF file
CONDITION,CONTROL for reading
The tool produced the following additional output:
cuffdiff v1.3.0 ()
cuffdiff --no-update-check -q -p 4 -c 1000 --FDR 0.050000 -N -b
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.