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Re: [scipion-users] Spider MDA Workflow not working again
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From: Gregory S. <sha...@gm...> - 2018-04-25 17:38:10
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PS. After downloading test data once, the tests can be run by normal users as well! :) To see all test datasets, run *scipion testdata --list* Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267542 <+44%201223%20267542> e-mail: gs...@mr... On Wed, Apr 25, 2018 at 6:24 PM, Patrick Goetz <pg...@ma...> wrote: > Thank you for clearing that up. Run as administrator, the test completes > successfully. > > On 04/25/2018 12:09 PM, Gregory Sharov wrote: > >> Hi Patrick, >> >> in your case all test data by default is located in >> /opt/scipion/data/tests folder. ScipionUserData is used only for user >> projects. Test data is supposed to be downloaded by admin/the person who >> installed scipion. >> >> Best regards, >> Grigory >> >> ------------------------------------------------------------ >> -------------------- >> Grigory Sharov, Ph.D. >> >> MRC Laboratory of Molecular Biology, >> Francis Crick Avenue, >> Cambridge Biomedical Campus, >> Cambridge CB2 0QH, UK. >> tel. +44 (0) 1223 267542 <tel:+44%201223%20267542> >> e-mail: gs...@mr... <mailto:gs...@mr...> >> >> >> On Wed, Apr 25, 2018 at 5:37 PM, Patrick Goetz <pg...@ma... >> <mailto:pg...@ma...>> wrote: >> >> Hi - >> >> Sorry for continuously spamming the list, but the Spider MDA >> Workflow test isn't working again, I just want to make sure I >> haven't introduced structural installation problems. >> >> First, I re-installed Scipion in /opt so that the users can access >> it, and made sure to install the spider package. Now running >> scipion as an ordinary user: >> >> /opt/scipion/scipion tests em.workflows.test_workflow_spiderMDA >> >> I get error messages and "2 Tests failed" again. Snooping around in >> the locally created ScipionUserData folder, I found this note in >> >> ~/ScipionUserData/projects/TestSpiderWorkflow/Runs/000002_ >> ProtImportParticles/logs/run.stdout: >> >> ------- >> Traceback (most recent call last): >> File "/opt/scipion/pyworkflow/protocol/protocol.py", line 186, in >> run >> self._run() >> File "/opt/scipion/pyworkflow/protocol/protocol.py", line 1104, >> in _run >> 'Protocol.run: Validation errors:\n' + '\n'.join(errors)) >> Exception: Protocol.run: Validation errors: >> There are no files matching the pattern >> /opt/scipion/data/tests/hemoglobin_mda/particles/*.spi >> ------- >> >> >> So apparently the test is trying to install data to >> /opt/scipion/data rather than ~/ScipionUserData ? >> >> Am I missing a configuration step that would instruct the system to >> process all data in the user's ScipionUserData folder? >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> <https://lists.sourceforge.net/lists/listinfo/scipion-users> >> >> >> >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
