Hi Matthias, we have encountered similar issues on our instance and we solved it (with help of Björn Grüning) differently: we have added <requirement type="package" version="2.7">python</requirement> in the requirements-tag of the corresponding xml file. Assuming that you use conda for dependency resolution, this could help. HTH, Eugen
On 10. Aug 2017, at 15:03, Matthias Bernt <m.bernt@ufz.de> wrote:
Hi,
I got an error from OpenMS which seems to be related to python3:
Fatal error: Exit code 1 (Error running OpenMS tool.) File "/gpfs1/data/galaxy_server/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/galaxyp/openms/42b843627623/openms/openms_wrapper.py", line 22 print "Running shell command %s" % command ^ SyntaxError: Missing parentheses in call to 'print'
Command line was
python /gpfs1/data/galaxy_server/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/galaxyp/openms/42b843627623/openms/openms_wrapper.py --executable 'DecoyDatabase' --config /gpfs1/data/galaxy_server/galaxy/jobs_dir/000/240/tmpYOuUf9
I would volunteer to improve this. But where can I find the sources? Would it be better to - use the compatibility import (easiest) - switch to print() - use logging
Best, Matthias
--
------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de
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