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 <nate@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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