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
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
Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann
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Hi Matthias, I think you're using an old version of the tool, the one at
https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_decoydatabase/178e00cf12d...
doesn't use a Python wrapper. The development repository is at
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms
Cheers, Nicola
On 10/08/17 14:03, Matthias Bernt 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
Hi Nicola and Bjoern,
thanks a lot for the informations. I'm just installing the suite.
Best, Matthias
On 10.08.2017 16:08, Nicola Soranzo wrote:
Hi Matthias, I think you're using an old version of the tool, the one at
https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_decoydatabase/178e00cf12d...
doesn't use a Python wrapper. The development repository is at
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms
Cheers, Nicola
On 10/08/17 14:03, Matthias Bernt 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
Hi Matthias,
please note that this repo is 4 years old. We have changed the wrappers quite a bit in the last years and now you have it here:
suite_openms
Or every tool has its own repo. Last update yesterday. Hope that helps, Bjoern
P.S. I have deprecated the old repo.
On 10.08.2017 15:03, Matthias Bernt 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
galaxy-dev@lists.galaxyproject.org
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Björn Grüning -
Matthias Bernt -
Nicola Soranzo -
Rempel, Eugen