Re: [galaxy-dev] startup bug in lib/galaxy/tools/toolbox/base.py

Dear Marius,

thanks for the information. You are right, there are entries in shed_tool_conf.xml for tools which I have uninstalled. I can manually remove them. I will file an issue because in the best case these entries would be removed when tools are uninstalled.

Best, Matthias

On 16.03.2017 11:10, Marius van den Beek wrote:

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.bernt@ufz.de mailto:m.bernt@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/bwa.xml
<http://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 <http://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
<http://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
<http://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
<http://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
<http://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
<http://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