Thanks, I will try this tomorrow. Fenglou
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. > > --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? >>>> >>> >>> >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > >
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