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
> 
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> 
>  http://lists.bx.psu.edu/
> 


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to