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 <feng...@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.ba...@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 <feng...@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.ba...@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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