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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