Hello Alejandro, Are you running this on a local or cloud instance? Have you run the workflow or the individual tools before? Do they exist on the server you are using? Checking In particular, the version of the Cuffdiff wrapper likely differs between the one you have installed (if this was recent) and the one in the workflow (it is an older version). Opening the workflow in the editor and updating the tool to the version on the server you are using (it will be in the tool pane, on the left), then saving it, will probably resolve the error. I've seen a similar issue to this one resolved this way before. Although, if your local is running the most recent distribution, this really shouldn't be an issue any longer. The current cloud ami may still present the issue, I'm not sure. Still - this is worth a try as potential quick path to a resolution on either. Please give this a test and let us know if you continue to have problems. I didn't notice anything else off. Jen Galaxy team On 2/25/14 2:44 PM, Alejandro Colaneri wrote:

I'm trying to run the attached workflow to run tophat followed by cuffdiff. But when I hit run a message saying server error appears and that is all (see screen shot attached). I have not clue where the error can be. It appear a very simple work flow. I will appreciate if someone give an idea of what can be wrong. Alejandro

___________________________________________________________ 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/

To search Galaxy mailing lists use the unified search at:

http://galaxyproject.org/search/mailinglists/

-- Jennifer Hillman-Jackson http://galaxyproject.org