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

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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