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Merged
merged 11 commits into from
Apr 22, 2025
Merged

Add kaiju #6908

merged 11 commits into from
Apr 22, 2025

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bernt-matthias
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@bernt-matthias bernt-matthias commented Apr 8, 2025 •
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  • shed file
  • tool data table
  • data manager
  • some more tools
    • kaiju-addTaxonNames,
    • kaiju-mergeOutputs,
    • kaiju2krona,
    • kaiju2table
    • maybe kaijux and kaijup

FOR CONTRIBUTOR:

  • I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • License permits unrestricted use (educational + commercial)
  • This PR adds a new tool or tool collection
  • This PR updates an existing tool or tool collection
  • This PR does something else (explain below)

@bernt-matthias bernt-matthias marked this pull request as draft April 8, 2025 14:44
@bernt-matthias bernt-matthias mentioned this pull request Apr 8, 2025
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@bernt-matthias bernt-matthias changed the title WIP: first commit of kaiju WIP: kaiju Apr 8, 2025
@bernt-matthias bernt-matthias changed the title WIP: kaiju Add kaiju Apr 14, 2025
@bernt-matthias bernt-matthias marked this pull request as ready for review April 14, 2025 14:56
bgruening
bgruening reviewed Apr 18, 2025
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Great, thanks a lot @bernt-matthias!

Just a few very small comments.

data_managers/data_manager_kaiju/.lint_skip Outdated
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remove?

tools/kaiju/kaiju-addTaxonNames.xml Outdated
@@ -0,0 +1,76 @@
<tool id="kaiju_addTaxonNames" name="kaiju-addTaxonNames" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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ID should be all lower-case, this makes configuration in TPV and elsewhere easier ...

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Should we have an additional linter for this?

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Mh, not sure ... maybe? Its very IUC specific I think.

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Not if TPV is the argument and you want to cover also non-IUC tools in TPV.
But in general it would be nice to have the possibility to include custom linters in planemo.

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Its convenience ... https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#tool-ids

Lets include it in linting behind some flag.

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We definitely need a linter .. forgot the 2nd capital letter :) I canceled the action and open a new PR.

bgruening
bgruening approved these changes Apr 22, 2025
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LGTM! But tests are not starting ...

@bernt-matthias bernt-matthias merged commit 176bcc0 into galaxyproject:main Apr 22, 2025
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@bernt-matthias bernt-matthias deleted the kajiu branch April 22, 2025 13:03
@mvdbeek
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mvdbeek commented Apr 22, 2025

Attention: deployment cancelled!

https://github.com/galaxyproject/tools-iuc/actions/runs/14595474660

@bernt-matthias bernt-matthias mentioned this pull request Apr 22, 2025
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@bgruening bgruening bgruening approved these changes

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3 participants
@bernt-matthias @mvdbeek @bgruening