Hi Fenglou,

In similar instances, I've simply compiled my own version of Python 2.7 and placed it in a cluster-wide filesystem, then used the environment_setup_file option in universe_wsgi.ini to ensure this version is used when jobs run.

--nate

On Thu, Feb 20, 2014 at 3:31 PM, Fenglou Mao <fenglou@gmail.com> wrote:

Thanks for the answer. I am talking to our sysadmin to upgrade cluster nodes from CentOS 5 to CentOS 6. 

Fenglou

On Feb 20, 2014, at 2:18 PM, Dannon Baker <dannon.baker@gmail.com> wrote:

Got it.  We dropped the simplejson egg during the last release (and any you find are holdovers from previous versions of galaxy) in favor of the stdlib module.  The relevant module from your find would have been simplejson-2.1.1, and the rest are unrelated.

If possible, I'd *really* recommend updating the python version on those nodes as future galaxy developments and tools may count on python 2.6+ (and not just for json, but syntax changes) being available.  Other than that, for those affected tools, you may want to manually revert the changes in revision 11967:0c5e20558f6b and add simplejson back into your galaxy.

That said, I'm working on adding the "anyjson" dependency that will allow json to fail through to any installed json library (whether stdlib, simplejson, etc), and that'll be available in galaxy-central reasonably soon.

On Thu, Feb 20, 2014 at 2:51 PM, Fenglou Mao <fenglou@gmail.com> wrote:

It is a little complicated here, The Galaxy server itself is running CentOS 6 with python 2.6, but the cluster nodes are running CentOS 5 with python 2.4. Mose jobs are running in the cluster nodes.

My questions is:

if there is a json module in galaxy-dist/eggs, why Galaxy is not picking it up? If we can do this, then we don't need to upgrade the cluster nodes, which is very difficult here.

Fenglou

On 20 February 2014 13:47, Dannon Baker <dannon.baker@gmail.com> wrote:

The json module is included in python's standard library since python 2.6, which is the minimum version of python Galaxy currently supports.  Are you using a python version older than that?

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