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Add kraken2 datatype#22455

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pvanheus wants to merge 6 commits into
galaxyproject:devfrom
pvanheus:add_kraken2_datatype
Draft

Add kraken2 datatype#22455
pvanheus wants to merge 6 commits into
galaxyproject:devfrom
pvanheus:add_kraken2_datatype

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@pvanheus
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The update in galaxyproject/tools-iuc#7257 for the kraken2 tool allows it to use a custom database passed as a parameter. Currently this uses the Directory datatype. This datatype allows a more specific input type to be specified and also allows a compressed archive to be uploaded and unpacked to the kraken2 database datatype.

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    1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

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return False


class Kraken2DatabaseArchive(CompressedArchive):
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I think there was some discussion about this already, but i think it'd be better to build an auto compressed version of Kraken2DatabaseDirectory instead ? We could also build an abstraction that allows just declaring the required files in the datatype config so we don't need code changes for this.

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Some guidance on how to do this would be much appreciated!

@mvdbeek mvdbeek marked this pull request as draft April 15, 2026 07:56
@mvdbeek mvdbeek moved this from Needs Review to In Progress in Galaxy Dev - weeklies Apr 15, 2026
@pvanheus pvanheus changed the title Add kraken2 datatype [DRAFT] Add kraken2 datatype Apr 23, 2026
@mvdbeek mvdbeek modified the milestones: 26.1, 26.2 May 19, 2026
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