I am designing some test and I have a problem, it works under the Galaxy web environment, but it doesn't work when I try to use it as a test case. Indeed I am trying other tests and they fail as well.
My test ./run_tests.sh -framework -id parallelism_bam_filter_reads says the next:
======================================================================
ERROR: filter reads ( parallelism_bam_filter_reads ) > Test-1
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/ralonso/galaxy/test/functional/test_toolbox.py", line 268, in test_tool
self.do_it( td )
File "/home/ralonso/galaxy/test/functional/test_toolbox.py", line 55, in do_it
raise e
RunToolException: Error creating a job for these tool inputs - {u'type': u'error', u'data': {u'input': u'History does not include a dataset of the required format / build'}}
And the other test ./run_tests.sh -framework -id compare_bam_as_sam
======================================================================
ERROR: compare_bam_as_sam ( compare_bam_as_sam ) > Test-1
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/ralonso/galaxy/test/functional/test_toolbox.py", line 268, in test_tool
self.do_it( td )
File "/home/ralonso/galaxy/test/functional/test_toolbox.py", line 37, in do_it
stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id )
File "/home/ralonso/galaxy/test/base/interactor.py", line 38, in stage_data_in_history
upload_wait()
File "/home/ralonso/galaxy/test/base/interactor.py", line 279, in wait
while not self.__history_ready( history_id ):
File "/home/ralonso/galaxy/test/base/interactor.py", line 297, in __history_ready
return self._state_ready( state, error_msg="History in error state." )
File "/home/ralonso/galaxy/test/base/interactor.py", line 356, in _state_ready
raise Exception( error_msg )
Exception: History in error state.
-------------------- >> begin captured logging << --------------------
Besides than it tries to migrate the database each time I try a test case and it takes too long. I have seen that you can use --db postgres but it doesn't work, I think this option should be user with --dockerize (that is not my case).
would you have any idea of what is going on?
Best regards
--
Roberto Alonso
Functional Genomics Unit
Bioinformatics and Genomics Department
Prince Felipe Research Center (CIPF)