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On usegalaxy.org, some tools fail if a history has a 'training' tag #361

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cat-bro opened this issue Jun 17, 2022 · 3 comments
Open

On usegalaxy.org, some tools fail if a history has a 'training' tag #361

cat-bro opened this issue Jun 17, 2022 · 3 comments

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@cat-bro
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cat-bro commented Jun 17, 2022

Describe the bug
For histories with the 'training' tag, uploading a file from a url fails with the following error:

Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tools/data_fetch.py", line 17, in <module>
    import bdbag.bdbag_api
ModuleNotFoundError: No module named 'bdbag'

I've shared the history here https://usegalaxy.org/u/cat-bro/h/datafetch-history. The first upload succeeds and the second fails because training tag has been added. I can't think of any other variables that could be affecting it.

@mvdbeek
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mvdbeek commented Jun 17, 2022

That is a deployment issue, I assume everything is mapped to singularity on the training destination.

@mvdbeek mvdbeek closed this as completed Jun 17, 2022
@mvdbeek mvdbeek transferred this issue from galaxyproject/galaxy Jun 17, 2022
@mvdbeek mvdbeek reopened this Jun 17, 2022
@cat-bro
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cat-bro commented Jun 17, 2022

I can no longer reproduce this. Data fetch works for histories with the training tag. Thanks Galaxy Main!

@cat-bro cat-bro closed this as completed Jun 17, 2022
@cat-bro cat-bro changed the title On usegalaxy.org, if a history has a 'training' tag, data fetch fails On usegalaxy.org, some tools fail if a history has a 'training' tag Jun 18, 2022
@cat-bro
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cat-bro commented Jun 18, 2022

Reopening this issue because there is another tool "UCSC Main table browser" failing with the training tag on the history, working otherwise.

tool id: ucsc_table_direct1
stderr:

Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/tools/data_source/data_source.py", line 16, in <module>
    from galaxy.datatypes import sniff
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/sniff.py", line 25, in <module>
    from typing_extensions import Protocol
ModuleNotFoundError: No module named 'typing_extensions'

@cat-bro cat-bro reopened this Jun 18, 2022
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