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…ld files are processed / downloaded in build stage then copied over from builder to app. App has symlinks between /opt/conda and /clair3 to make sure consistency is met for Staph-B scripts.
erinyoung
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Mar 13, 2026
build-files/clair3/2.0.0/README.md
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| autoconf 2.72 pl5321hbb4ee43_1 conda-forge | ||
| automake 1.17 pl5321ha770c72_0 conda-forge |
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It looks like a lot of the compiler software made it to the app stage, such as autoconf and automake. These software aren't needed at runtime, so it will help reduce the image size if we exclude them from the app stage.
…uv/pip packages. Reincluded symlinks that were required.
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Pull Request (PR) checklist:
docker build --tag samtools:1.15test --target test docker-builds/build-files/samtools/1.15)docker-builds/build-files/spades/3.12.0/Dockerfile)build-files/shigatyper/2.0.1/test.sh)docker-builds/build-files/spades/3.12.0/README.md)Update to Clair3 for version 2.0.0. This pull request includes the Dockerfile and README.md updated for v2.0.0. I refactored the builder stage a bit so that another micromamba install step was not needed. I included symlinks from /clair3 to /opt to make sure that we had backwards compatibility with what we produced before.
The README.md is longer than 30 lines since I wanted to include the micromamba list and models downloaded.