Vipin TS wrote:
> Hi all,
>
> Last day we upgraded our galaxy service computing cluster nodes operating
> system from Ubuntu hadry to lucid 10.4. We updated python eggs and now
> getting an Warning message, it apparently kills the galaxy jobs. Warning
> message as follows:
>
> /home/abc/galaxy/lib/galaxy/eggs/__init__.py:332: UserWarning: Unbuilt
> egg for pytz [unknown version] (/usr/lib/python2.6/dist-packages)
> env = pkg_resources.Environment( platform=pkg_resources.get_platform() )
>
> >From the warning message I can see that the problem with unbuilt egg for
> pytz module. Before approaching you I googled the same and got a good thread
> which explains similar kind of issues (
> https://bugs.launchpad.net/ubuntu/+source/distribute/+bug/576434). I
> followed #9 from TJ and made a work around and unfortunately no luck. Does
> anyone had a problem with this before, if yes I like to hear from you that
> how do u managed to get rid of the warning message.
Hi Vipin,
If you haven't come up with a solution for this from the Ubuntu side, there
should at least be a workaround within Galaxy (this is untested).
In lib/galaxy/eggs/__init__.py, somewhere near the top:
import warnings
inside get_env():
def get_env():
with warnings.catch_warnings():
warnings.simplefilter("ignore")
env = pkg_resources.Environment( search_path='',
platform=pkg_resources.get_platform() )
for dist in pkg_resources.find_distributions( os.path.join( galaxy_dir,
'eggs' ), False ):
env.add( dist )
return env
--nate
>
> Many thanks,
>
> Vipin T S
> Friedrich Miescher Laboratory
> of the Max Planck Society
> Spemannstrasse 39, 72076
> Tuebingen, Germany
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