> 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 Best, J. ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
