Re: [galaxy-dev] openms python3 & print
Hi Matthias, we have encountered similar issues on our instance and we solved it (with help of Björn Grüning) differently: we have added python 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 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.be...@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 > --- > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] openms python3 & print
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/178e00cf12d7 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 -- --- 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.be...@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 --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] openms python3 & print
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 > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] openms python3 & print
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/178e00cf12d7 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 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] openms python3 & print
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.be...@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 --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
