On Thu, May 26, 2011 at 2:42 PM, Bossers, Alex <alex.boss...@wur.nl> wrote:
> PS: 2 is STDERR and 1 is STDOUT. One could do a redirect of STDERR to STDOUT
> and STDOUT to a logfile. You won’t get a red box though when errors occur!

Right - if you need to detect an error state via the return code,
currently you have to do this with a wrapper script.

If you don't ever expect any errors, then you can treat stderr
as an output, or just redirect to to /dev/nul - but I don't like that
idea - silent failures are bad.

I regard fixing issue 325 as one of the top priorities in Galaxy, but
in the short term I'd settle for treating any output on stderr OR
a non-zero return code as a failure. i.e. Something like this patch,
even if more work is needed for PBS jobs:
https://bitbucket.org/galaxy/galaxy-central/issue/325/#comment-331776

Peter

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