By default Galaxy checks stderr, if it's not empty - returns an error. So if
your tool doesn't fail (returns 0) but you print something to stderr , your
tool will still fail in Galaxy. There's stderr_wrapper.py workaround for
that.
On the other hand, if you tool returns non zero but doesn't use stderr --
Galaxy ignores tools return value.
There are two ways around that:
1. Galaxy has exit_code tag to specify which exit codes to handle
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cexit_code.3E_tag_set
So in my tool.xml I have:
stdio
exit_code range=1:255 level=fatal description=XLICTRecon.exe
Exception /
/stdio
2. Simple workaround in the Python wrapper, print something to stderr if
the tool returns an error:
returncode = subprocess.call(cmd)
if(returncode):
sys.stderr.write('Error: returned ' + str(returncode))
-Alex
-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.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 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:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax
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?
Peter
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