Hi, I found the solution. I had to update the Tophat wrapper XML from Galaxy repository, in order to be computable with the newer version of Tophat that we have.
Hope this post will be informative to someone. Thanks, Liram From: VARDI,LIRAM (A-Labs,ex1) Sent: Tuesday, May 15, 2012 5:57 PM To: Galaxy Dev (galaxy-...@bx.psu.edu) Cc: BEN-DOR,AMIR (A-Labs,ex1); TSALENKO,ANYA (A-Labs,ex1) Subject: Internal Server Error when using Galaxy API Hi all, I have a strange problem when I am trying to run workflow using Galaxy API. If the workflow contains Tophat for Illumina, then when I am trying to use the "submit" API script in order to execute this workflow on some input dataset, I am strangely getting this HTTP error: "Error. 500 Internal Server Error The server has either erred or is incapable of performing the requested operation." Although the server has returned an error message, when I checked the "saved histories" I could notice that the job was successfully submitted and it is running! When I removed TopHat from the workflow, no error was returned... The thing is that I need the "dictionary" that is returned by the "submit" script. Has anyone encountered this problem before and know how to solve it? Thanks in advance! Liram
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