u.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Peter Cock
Sent: Tuesday, 23 October 2012 2:30 AM
To: David Hoover
Cc: Galaxy Dev
Subject: Re: [galaxy-dev] determination of errors
On Mon, Oct 22, 2012 at 4:23 PM, David Hoover wrote:
> How does Galaxy determine that a job h
On Mon, Oct 22, 2012 at 4:23 PM, David Hoover 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 o
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%20st
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
