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Add zellkonverter to wilms-06 environment #890

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sjspielman
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Towards #866

We need to update the link to the CELLxGENE kidney reference used in this module to the h5ad AnnData file rather than the rds Seurat file, since CELLxGENE will stop supporting Seurat objects at the end of 2024.

For this, we'll need the zellkonverter package. This PR updates the renv environment so that the Docker image can be updated, which will allow for a 2nd PR that downloads and converts the h5ad file. This PR also restores the R version to 4.4.0, the official OpenScPCA R version, from 4.4.1 which ended up in there at one point. Finally, I also updated the docker GHA to run on feature/* branches so will actually accomplish what we want it to do!

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👍🏻 if checks pass 🏁

@sjspielman
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I need to move zellkonverter into components/dependencies.R for now!

…also removed packages from dependencies.R that don't need to be there since they are in other scripts explicitly
@jashapiro
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For the docker image, you probably want to add a RUN step like the one in doublet-detection and elsewhere that pre-downloads the zellkonverter conda environment:

# Complete installation of zellkonverter conda env
ENV BASILISK_EXTERNAL_DIR /usr/local/renv/basilisk
RUN Rscript -e "proc <- basilisk::basiliskStart(env = zellkonverter::zellkonverterAnnDataEnv(), testload = 'anndata'); \
basilisk::basiliskStop(proc); \
basilisk.utils::cleanConda()"

@sjspielman
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sjspielman commented Nov 18, 2024

This has passed CI. The only change since was adding a newline for GitHub appeasement, so we can merge before all checks complete.
edit: depending on my permissions :)

@sjspielman sjspielman merged commit a275005 into AlexsLemonade:feature/wilms-tumor-06-azimuth Nov 18, 2024
4 of 5 checks passed
@sjspielman sjspielman deleted the sjspielman/866-update-renv-docker branch November 18, 2024 16:00
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3 participants