Thanks, I will try this tomorrow.
On 20 February 2014 22:32, Nate Coraor <n...@bx.psu.edu> wrote:
> 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.
> 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.
>> 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
>> 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.
>>> 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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