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/
