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Update artic for new medaka models #984
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@jessicarowell , it looks like adjusting the base image back to 1.4.8 resolved the issue. |
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jessicarowell
approved these changes
May 31, 2024
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There isn't a new version of artic, but there is a new version of medaka.
Artic is showing its age. Originally, 1) the github repo was downloaded, 2) the environmental file was used to create a conda environment, 3) pip was used to install artic. I kept running into environment incompatibilities, so this image now uses micromamba to install artic entirely and the github archive is downloaded only for testing.
The medaka on conda (and installed in the step above) is an old version, and I'm most interested in the new medaka models. I do like how conda installs all of medaka's dependencies, though, even if its for an old version. Therefore, there is a reinstall of medaka using pip afterward followed by a pip install of pyabpoa. I do not fully know why pyabpoa needs to be installed last, but there are errors thrown if installed with the same line of medaka. pyabpoa does not get installed with conda for whatever reason.
Pull Request (PR) checklist:
docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15
)spades/3.12.0/Dockerfile
)shigatyper/2.0.1/test.sh
)spades/3.12.0/README.md
)