On Mon, Oct 22, 2012 at 4:23 PM, David Hoover <hoove...@helix.nih.gov> wrote:
> How does Galaxy determine that a job has failed?

It now depends on the individual tool's XML file.

> Does it simply see if the STDERR is empty?

Why default, yes. The tool's XML can specify particular regexs
to look for, or to decide based on the return code - but for the
time being most of the tools still just look at stderr. See:

> What happens if an application normally outputs to STDERR?

Either use the new functionality in the XML definition, or what
older Galaxy tools did was a wrapper script to hide/redirect
stderr to avoid false positives.

> 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.

In which case the user should see those errors and be able
to do something about it, right?

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