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-requ...@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
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