How does Galaxy determine that a job has failed?  Does it simply see if the 
STDERR is empty?  What happens if an application normally outputs to STDERR?

This is a problem for our local installation, as I have enabled it to run as 
the local user on the backend cluster.  If a user has an error in the .bashrc 
file, it will automatically write to STDERR, and all jobs, no matter what, are 
labelled as failing.

David Hoover
Helix Systems Staff
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