On Nov 2, 2012, at 4:42 PM, Carlos Borroto <carlos.borr...@gmail.com> wrote:
> On Fri, Nov 2, 2012 at 3:58 PM, Carlos Borroto <carlos.borr...@gmail.com> > wrote: >> On Fri, Nov 2, 2012 at 9:53 AM, Oleksandr Moskalenko <o...@hpc.ufl.edu> >> wrote: >>> >>> The dynamic runner is alive and well thanks to the continuous work of the >>> author John Chilton and others. For instance, yesterday John committed code >>> to galaxy-central that propagates tracebacks from the dynamic job runner's >>> job rules script to the logs and also allows us to raise explicit >>> exceptions from the job rules script thus making it possible to fail a job >>> and print an arbitrary message in the job history's error message as well >>> as making it much easier to debug the job rules. >>> >> >> Great!. > > First bump: > > galaxy.jobs.handler DEBUG 2012-11-02 16:37:00,728 Loaded job runner: > galaxy.jobs.runners.drmaa:DRMAAJobRunner > galaxy.jobs.handler ERROR 2012-11-02 16:29:00,415 Job runner is not > loadable: galaxy.jobs.runners.dynamic > Traceback (most recent call last): > File "/local/opt/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", > line 375, in _load_plugin > module = __import__( module_name ) > ImportError: No module named dynamic > > In my universe_wsgi.ini: > > start_job_runners = drmaa,dynamic > > I get the same error with -dist and -central. Alex, are you sure > dynamic job runner is already included? Should I pull something from > somewhere else? Hi Carlos, Dynamic job runner is a layer on top of either the pbs or the drmaa runner that actually submits the job: start_job_runners = drmaa default_cluster_job_runner = dynamic:///python/default_runner where "default_runner" is a procedure you define in the job rules script. Then, you can set the correspondence per tool as in upload1 = dynamic:///python/upload1 ncbi_blastn_wrapper = dynamic:///python/ncbi_blastn ncbi_blastp_wrapper = dynamic:///python/ncbi_blastp and so on or just figure out the tool_id in the default_runner procedure. Regards, Alex ___________________________________________________________ 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/
