Menu
▾
▴
Re: [scipion-users] Spider MDA Workflow not working again
|
From: Pablo C. <pc...@cn...> - 2018-04-26 08:43:55
|
Thanks Gregory, and no worries Patrick. emails here are welcome and are a good source of "learning" or discovering issues. Regarding the test data, you can askf for tha list, as Gregory pointed out, but you can also download them. It might be worth "open up" the test data folder, depending on your "security" policies: "/opt/scipion/data/tests" --> give writing, reading permissions to all. Al the best, Pablo. On 25/04/18 19:37, Gregory Sharov wrote: > 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 <tel:+44%201223%20267542> > e-mail: gs...@mr... <mailto:gs...@mr...> > > On Wed, Apr 25, 2018 at 6:24 PM, Patrick Goetz <pg...@ma... > <mailto: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...> > <mailto:gs...@mr... > <mailto:gs...@mr...>> > > > On Wed, Apr 25, 2018 at 5:37 PM, Patrick Goetz > <pg...@ma... <mailto:pg...@ma...> > <mailto: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...> > <mailto:sci...@li... > <mailto:sci...@li...>> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > <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... > <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... > <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 |
