Hi,

I posted this question to biostars but didn't get an answer....

Is it possible to use "planemo test" functionality on an SGE cluster? I can
correctly run a custom tool on an SGE cluster when I manually run a job
through the galaxy interface. If I change the job_conf.xml so that the job
is run locally, I can use "planemo test" successfully, but if I change the
job_conf.xml so that Galaxy uses the SGE cluster, planemo fails:

Traceback (most recent call last):
  File "/remote/home/galaxyd/galaxy-test-SGE/test/functional/test_toolbox.py",
line 289, in test_tool
    self.do_it( td )
  File "/remote/home/galaxyd/galaxy-test-SGE/test/functional/test_toolbox.py",
line 38, in do_it
    stage_data_in_history( galaxy_interactor, testdef.test_data(),
test_history, shed_tool_id )
  File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py",
line 43, in stage_data_in_history
    upload_wait()
  File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py",
line 280, in wait
    while not self.__history_ready( history_id ):
  File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py",
line 298, in __history_ready
    return self._state_ready( state, error_msg="History in error state." )
  File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py",
line 361, in _state_ready
    raise Exception( error_msg )
Exception: History in error state.
-------------------- >> begin captured stdout << ---------------------
History with id 2891970512fa2d5a in error - summary of datasets in error below.
--------------------------------------
| 1 - MTB_Genes.fasta (HID - NAME)
| Dataset Blurb:
|  tool error
| Dataset Info:
|  The cluster DRM system terminated this job
| Dataset Job Standard Output:
|  *Standard output was empty.*
| Dataset Job Standard Error:
|  *Standard error was empty.*
|
--------------------------------------

--------------------- >> end captured stdout << ----------------------

Is this a problem with my configuration or a limitation of planemo?


Thanks!
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