Yes, by default STDERR is used for determining error state.  Older tools likely 
haven't been updated to use it, but there does exist functionality for doing 
more sophisticated error detection (exit codes, regex, etc), see the wiki here: 
 http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr

-Dannon


On Oct 22, 2012, at 11:23 AM, David Hoover <hoove...@helix.nih.gov> wrote:

> 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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