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.be...@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
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> Phone +49 341 235 482296,
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