On Mar 30, 2012, at 5:53 AM, Alban Lermine wrote:
Hi,
It seems that PYTHONPATH isn't set when galaxy start.. (according to
http://osdir.com/ml/galaxy-development-source-control/2011-11/msg00035.html)
Should I search this way ?
Hi Alban,
Galaxy should be setting PYTHONPATH itself, it's only necessary to set it if
you are trying to run some of the tools from outside Galaxy. Could you set
cleanup_job = never in your Galaxy config and check the PBS script (the path to
it should be output to the log when you run a job). The script should have
this at the top:
GALAXY_LIB=/path/to/galaxy-dist/lib
if [ $GALAXY_LIB != None ]; then
if [ -n $PYTHONPATH ]; then
export PYTHONPATH=$GALAXY_LIB:$PYTHONPATH
else
export PYTHONPATH=$GALAXY_LIB
fi
fi
--nate
Thanks by advance,
Alban
Alban Lermine wrote:
Hi,
I'm running these tools on a cluster..
Alban
Emil Bouvier wrote:
Alban,
Are you running these tools on a cluster, or on a local system?
Dave B.
On 3/19/12 6:55 AM, Alban Lermine wrote:
Hi,
I have the same error message for multiple tools (GFFtoBED,
BEDtoBIGBED,BAMtoSAM,...):
/from galaxy import eggs
ImportError: No module named galaxy
It's happening only since the last upgrade, do you know what is going
wrong?
Thanks,
Alban
/
--
Alban Lermine
Unité 900 : Inserm - Mines ParisTech - Institut Curie
« Bioinformatics and Computational Systems Biology of Cancer »
11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France
Tel : +33 (0) 1 56 24 69 84
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