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
to get some more opinions on
this.
Best,
Marius
On 16 March 2017 at 09:33, Matthias Bernt <m.bernt(a)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.bernt(a)ufz.de,
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/