Hi Matthias,

so typically what's happening there is that there is no
tool_shed_respository entry in the database for this tool.
I see this in my development instance when I setup a new database, but keep
my old shed_tool_conf.xml.

If you want to get rid of these errors you can uninstall the tools in
question and install them again from the toolshed.

It could be worth thinking about relaxing the assumption that tools in the
shed_tool_conf.xml should have an entry in the database.
I'd encourage you to open an issue on
https://github.com/galaxyproject/galaxy/issues to get some more opinions on
this.


Best,
Marius

On 16 March 2017 at 09:33, Matthias Bernt <m.be...@ufz.de> wrote:

> Dear galaxy developers,
>
> I sent this originally to the galaxy-bugs list and was asked to forward
> this also to this list. What is the best way to report bugs? There is
> galaxy-bugs, galaxy-dev and also the issue tracker on galaxy.
>
> During startup of my galaxy 17.01 installation an error message pops up:
>
> galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,605 Error reading tool
> from path: toolshed.g2.bx.psu.edu/repos/devteam/bwa/53646aaaafef/bwa/bw
> a.xml
> Traceback (most recent call last):
>   File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line 560,
> in _load_tool_tag_set
>     tool.tool_shed = tool_shed_repository.tool_shed
> AttributeError: 'NoneType' object has no attribute 'tool_shed'
>
> Seems that tool_shed_repository is still None at this point. This happens
> for some tools.
>
> galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,764 Error reading tool
> from path: toolshed.g2.bx.psu.edu/repos/devteam/bwa/53646aaaafef/bwa/bw
> a-mem.xml
> Traceback (most recent call last):
>   File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line 560,
> in _load_tool_tag_set
>     tool.tool_shed = tool_shed_repository.tool_shed
> AttributeError: 'NoneType' object has no attribute 'tool_shed'
> galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,768 Error reading tool
> from path: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/a00a6402d09a/fas
> tqc/rgFastQC.xml
> Traceback (most recent call last):
>   File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line 560,
> in _load_tool_tag_set
>     tool.tool_shed = tool_shed_repository.tool_shed
> AttributeError: 'NoneType' object has no attribute 'tool_shed'
> galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,773 Error reading tool
> from path: toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_qualit
> y/25c24379693a/fastq_trimmer_by_quality/fastq_trimmer_by_quality.xml
> Traceback (most recent call last):
>   File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line 560,
> in _load_tool_tag_set
>     tool.tool_shed = tool_shed_repository.tool_shed
> AttributeError: 'NoneType' object has no attribute 'tool_shed'
> galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,779 Error reading tool
> from path: toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_qualit
> y/04a609b0fdf6/fastq_trimmer_by_quality/fastq_trimmer_by_quality.xml
> Traceback (most recent call last):
>   File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line 560,
> in _load_tool_tag_set
>     tool.tool_shed = tool_shed_repository.tool_shed
> AttributeError: 'NoneType' object has no attribute 'tool_shed'
> galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,788 Error reading tool
> from path: toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer/e0cfb5a70
> 3ce/fastq_trimmer/fastq_trimmer.xml
> Traceback (most recent call last):
>   File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line 560,
> in _load_tool_tag_set
>     tool.tool_shed = tool_shed_repository.tool_shed
> AttributeError: 'NoneType' object has no attribute 'tool_shed'
> galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,793 Error reading tool
> from path: toolshed.g2.bx.psu.edu/repos/geert-vandeweyer/fastq_qc_trimm
> er/cba6282b5dc8/fastq_qc_trimmer/Paired_fastQ_trimmer.xml
> Traceback (most recent call last):
>   File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line 560,
> in _load_tool_tag_set
>     tool.tool_shed = tool_shed_repository.tool_shed
> AttributeError: 'NoneType' object has no attribute 'tool_shed'
>
> 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
>
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> Wilfried Kraus
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> Prof. Dr. Dr. h.c. Georg Teutsch
> Administrative Geschäftsführerin/ Administrative Managing Director:
> Prof. Dr. Heike Graßmann
> -------------------------------------------
>
>
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