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/bwa.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/bwa-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/fastqc/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_quality/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_quality/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/e0cfb5a703ce/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_trimmer/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

Sitz der Gesellschaft/Registered Office: Leipzig
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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
-------------------------------------------

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