Galaxy assumes that tools that write to stderr indicate failure. There's apparently some way to set up regexps to get around that, but I don't know where to do that (or if indeed that would work). Command-line debugging works some, except when the web server's environment (path, etc.) differs from command line. Or the problem is in how Galaxy interprets output; e.g. "stderr means error" as described above. John Chilton suggested I try using the logging facility, but binary.py throws an exception when I try to do that: An error occurred running this job:uploaded csra file No handlers could be found for logger "galaxy.datatypes.binary" So it's back to square one. Debugging without even a working print statement is pretty difficult. Even trying log = logging.getLogger() or log = logging.getLogger('wsgi') produces exceptions. I would assume there'd be a way to set up logging in universe_wsgi.ini, but none of the logging parameters seem to set up a root logger that tools can use. --mj On 10/12/12 10:55 AM, galaxy-dev-request@lists.bx.psu.edu wrote:

You can get to the captured stdout/stderr in the UI by clicking the info (i) button for the dataset. The way I would normally debug outside of the Galaxy UI is to take the command line generated by Galaxy (which should be logged) and run it outside Galaxy.

-- jt