openms python3 & print

classic Classic list List threaded Threaded
5 messages Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

openms python3 & print

Matthias Bernt
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,
[hidden email], 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/
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: openms python3 & print

Rempel, Eugen
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 <[hidden email]> 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,
> [hidden email], 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/
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: openms python3 & print

Nicola Soranzo-2
In reply to this post by Matthias Bernt
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/
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: openms python3 & print

Björn Grüning-3
In reply to this post by Matthias Bernt
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/
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: openms python3 & print

Matthias Bernt
In reply to this post by Nicola Soranzo-2
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,
[hidden email], 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/
Loading...