On Thu, Oct 23, 2008 at 4:11 PM, Nate Coraor <nate@bx.psu.edu> wrote:

Sean Davis wrote:

...

/home/www/galaxy/lib/galaxy/eggs/__init__.py:529: UserWarning: Module simplejson was already imported from

/usr/local/lib64/python2.5/site-packages/simplejson-1.7.1-py2.5.egg/simplejson/__init__.py, but /home/www/galaxy/eggs/py2.5-noplatform/simplejson-1.5-py2.5.egg is being added to sys.path pkg_resources.working_set.require( "%s==%s" % ( name, egg.get_vertag() ) )

I got this when doing Get Data->UCSC table browser->get BED of ucsc known genes; the download failed. It looks like there are some version confusions here.

Any suggestions?

Hi Sean,

This is a bug with the way we handle dependency versions, but for the short term, a simple solution is to remove the conflicting egg (from /usr/local).

Thanks, Nate. Removing the conflicting egg isn't really an option (the host runs multiple sites), but it is good to know what the problem is. I guess will need to go with a custom python installation for running galaxy. Sean

On Fri, Oct 24, 2008 at 12:37 PM, Nate Coraor <nate@bx.psu.edu> wrote:

Sean Davis wrote:

...

Thanks, Nate. Removing the conflicting egg isn't really an option (the host runs multiple sites), but it is good to know what the problem is. I guess will need to go with a custom python installation for running galaxy.

Sean,

I've tracked the bug down and pushed a fix to hg. Please update your source and try again. Hopefully you can avoid having to run a custom Python.

Great. Thanks so much for the information and the unbelievably quick fix! Sean