On Aug 8, 2012, at 12:06 PM, Rui Wang wrote:

> Hi Nate,
> 
> Thanks for the suggestion. Our cluster does not belong to us so we had to 
> request that to be added by their sysadmin. Before that we modified the code 
> in a few scripts to ignore the deprecation warning, that also fixed the 
> problem, should we remove these mods now since the new pytz is installed?

If you upgrade pytz, the DeprecationWarnings should go away, and then you would 
not need to handle them.

> A separate question, do you happen to know where I could find the 
> instructions for setting up job submission for PBS/torque? There are pieces 
> and bits information here and there but I didn't see any comprehensive one...

Our documentation is at:

    http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster

If there's something missing from this, please let us know.

Thanks,
--nate

> 
> Best Regards,
> Rui
> 
> On Wed, Aug 8, 2012 at 7:54 AM, Nate Coraor <n...@bx.psu.edu> wrote:
> On Aug 2, 2012, at 1:59 PM, Rui Wang wrote:
> 
> > Hi All,
> >
> > we are installing a local galaxy instance but we met something puzzling.
> >
> > we are running galaxy on cent os 5.x and python 2.6.1. when we tried to 
> > upload
> > data, it failed with the message
> >
> >
> > *************************************************************************
> > Dataset generation errors
> >
> > Dataset 5: brain.fa
> > Tool execution generated the following error message:
> >
> > /usr/usc/python/2.6.1/lib/python2.6/site-packages/pytz/tzinfo.py:5: 
> > DeprecationWarning: the sets module is deprecated from sets import Set
> > *************************************************************************
> >
> > However, when we tried to use the galaxy version tied to the OS, which is 
> > 2.4.3, we
> > were able to upload successfully. Did anyone have the same experience?
> >
> > Any advice will be greatly appreciated.
> 
> Hi Rui,
> 
> I'd suggest upgrading your version of pytz with `easy_install --upgrade 
> pytz`.  Newer versions should correctly handle importing sets.
> 
> --nate
> 
> >
> > Thanks,
> > Rui
> >
> >
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> 
> 


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