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>
>> On Fri, Nov 2, 2012 at 9:53 AM, Oleksandr Moskalenko <o...@hpc.ufl.edu>
>>> 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.
> First bump:
> galaxy.jobs.handler DEBUG 2012-11-02 16:37:00,728 Loaded job runner:
> 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?
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.
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