This looks like some script is correct locally but not on the cluster.
It looks like the script has some error (like are modules available
locally but not on the cluster). At any rate this error is being
reported on standard error and the script is continuing to run (hence
the datasets being written properly) but Galaxy is still treating the
standard error message as a error.
I think fixing this is a matter of hunting down this problematic
script. It could be something in your or your Galaxy user's .bashrc
script for instance. The easy was to determine this is to do a qsub or
srun on the command line as your Galaxy user and see if the same
message is printed in the job's standard error.
If it is not that - it is probably a Galaxy configuration problem -
either it is a tool specific problem (some wrapper script is invalid
on the cluster) or a cluster wide configuration problem. If lots of
tools are experiencing this problem it is probably the latter and I
would imagine you have setup an environment_setup_file in
universe_wsgi.ini that is invalid for the cluster or you are using the
newer <env> tags in job_conf.xml.
If none of those is the problem - than it is probably a problem with
an env.sh file (either manually setup or configured via the tool shed)
or maybe a job metrics problem.
I hope this helps.
On Mon, Sep 1, 2014 at 9:54 AM, Sandra Derozier
I try to set up functional tests on different tools on my Galaxy portal.
When I run functional tests locally everything works fine. But when I run
them on the cluster it failed with this message :
/bin/sh: module: line 1: syntax error: unexpected end of file
/bin/sh: error importing function definition for `module'
The execution on the cluster is ok but the dataset state is set to ERROR.
The DIFF between the expected result and the obtained result is null.
Indeed, this two files are the same.
As I do not know what the problem is: do you have an idea?
Unité Mathèmatique, Informatique et Génome (MIG)
Domaine de Vilvert
78352 Jouy-en-Josas Cedex
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