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khmer v3 does not work the same as v2 and is incompatible #53444

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@dr-joe-wirth dr-joe-wirth commented Jan 23, 2025

primerForge does not work with khmer v3. I do not know what has changed between versions, but it does not generate the same results it used to. khmer v2.1 does work. I have restricted the build to reflect this.

@mencian the recipes for both primerforge 1.5.2-0 and primerforge 1.5.3-0 are broken because of this incompatibility. It passes the bioconda recipe checks, but the unit tests fail.

related to #48898 and #53433

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@bioconda-bot please fetch artifacts

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Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
noarch primerforge-1.5.3-pyhdfd78af_1.tar.bz2 noarch.zip GitHub Actions
showYou may also use conda to install after downloading and extracting the zip file. conda install -c ./packages <package name>

Docker image(s) built:

Package Tag CI Install with docker
primerforge 1.5.3--pyhdfd78af_1 GitHub Actions
showImages are in the linux-64 zip file above.gzip -dc images/primerforge---1.5.3--pyhdfd78af_1.tar.gz | docker load

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i am going to run unit tests on this build to ensure it is working. i will review changes once i have confirmed it runs.

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