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