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?

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...

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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