Updating bacterial_genomics/amr_gene_detection from 1.1.5 to 1.1.6

[hugolefeuvre]

This PR closes this PR : #782
Increase the version of Tooldistillator to 1.0.0+galaxy1. I am opening a new PR reusing the changes made by @clsiguret on the old one.
Thanks !

FOR CONTRIBUTOR:

• I have read the Adding workflows guidelines
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FOR REVIEWERS:

• .dockstore.yml: file is present and aligned with creator metadata in workflow. ORCID identifiers are strongly encouraged in creator metadata. The .dockstore.yml file is required to run tests
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[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

• ❌ amr_gene_detection.ga_0

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.0+galaxy1 (version 1.0.0+galaxy1), toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.0+galaxy1 (version 1.0.0+galaxy1)","err_code":0}
    

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

• ❌ amr_gene_detection.ga_0

  Execution Problem:

  • Failed to upload data, upload state is [error].
    

[hugolefeuvre]

Error is the same (https://github.com/galaxyproject/iwc/actions/runs/17273630608/job/49024809466?pr=939#step:7:3383) as reported in the original PR with DB in cvmfs going wrong with empty SHA.
It has been solved by adding this galaxyproject/usegalaxy-playbook@5447308 for usegalaxy.org and it works. Do you think it's possible to re-use this in our case ?

[mvdbeek]

Yes, can you open a PR to the tool that adds those environment variables ? Alternatively I think the container can be rebuilt with a newer git version.

[hugolefeuvre]

Yes, can you open a PR to the tool that adds those environment variables ? Alternatively I think the container can be rebuilt with a newer git version.

Which method do you think is the best and most reusable/FAIR ?
I'm not sure I fully understand what you mean. Your first proposal is to make changes directly to the starAMR repository, and the second is simply to change the git version of the container ?

[mvdbeek]

The easiest fix is this on line 37: https://github.com/galaxyproject/tools-iuc/blob/main/tools/staramr/staramr_search.xml#L37

export GIT_CONFIG_COUNT=1 GIT_CONFIG_KEY_0=safe.directory GIT_CONFIG_VALUE_0=* &&

You could also specify a minimum git version in the conda recipe that is the base for the container here: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/staramr/meta.yaml#L36