Question: Galaxy SGE Cluster, Planemo testing?
gravatar for danielfortin86
2.8 years ago by
United States
danielfortin86110 wrote:


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/", line 289, in test_tool
    self.do_it( td )
  File "/remote/home/galaxyd/galaxy-test-SGE/test/functional/", 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/", line 43, in stage_data_in_history
  File "/remote/home/galaxyd/galaxy-test-SGE/test/base/", line 280, in wait
    while not self.__history_ready( history_id ):
  File "/remote/home/galaxyd/galaxy-test-SGE/test/base/", 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/", 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?



tests cluster planemo sge • 898 views
ADD COMMENTlink modified 2.7 years ago • written 2.8 years ago by danielfortin86110


I've been unable to resolve this issue. I'd really like to be able to use "planemo test" in order to run tests. I'm trying to transition our galaxy instance over to use SGE but am unsure whether all of our custom scripts will execute correctly. For this reason I want to use the "planemo test" functionality on the SGE cluster. No matter what I've tried, the tests always fail even though running the same scripts through the galaxy interface completes successfully. Does anyone have any suggestions?


ADD REPLYlink written 2.7 years ago by danielfortin86110
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