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
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