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Add zellkonverter to wilms-06 environment #890
Add zellkonverter to wilms-06 environment #890
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👍🏻 if checks pass 🏁
I need to move |
…also removed packages from dependencies.R that don't need to be there since they are in other scripts explicitly
For the docker image, you probably want to add a RUN step like the one in OpenScPCA-analysis/analyses/doublet-detection/Dockerfile Lines 71 to 75 in ad8b1dc
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This has passed CI. The only change since was adding a newline for GitHub appeasement, so we can merge before all checks complete. |
a275005
into
AlexsLemonade:feature/wilms-tumor-06-azimuth
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 therenv
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 onfeature/*
branches so will actually accomplish what we want it to do!