On Thu, May 26, 2011 at 2:42 PM, Bossers, Alex <Alex.Bossers@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