Add rOpenScPCA to renv/docker in ewing module

[allyhawkins]

Purpose/implementation Section

Please link to the GitHub issue that this pull request addresses.

Towards #878

What is the goal of this pull request?

Here I'm just adding rOpenScPCA to the lock file for renv and subsequently the Docker image. I also noticed a typo in the GHA for building the ewing's docker image that I fixed.

Briefly describe the general approach you took to achieve this goal.

Installed the package and then took a snapshot.

If known, do you anticipate filing additional pull requests to complete this analysis module?

Yes!
Next up, I'll be updating the cluster template to use the functions in rOpenScPCA. I also plan on incorporating Leiden clustering results to the plots now that we have that functionality in rOpenScPCA.

Author checklists

Analysis module and review

• This analysis module uses the analysis template and has the expected directory structure.
• The analysis module README.md has been updated to reflect code changes in this pull request.
• The analytical code is documented and contains comments.
• Any results and/or plots this code produces have been added to your S3 bucket for review.

Reproducibility checklist

• Code in this pull request has been added to the GitHub Action workflow that runs this module.
• The dependencies required to run the code in this pull request have been added to the analysis module Dockerfile.
• If applicable, the dependencies required to run the code in this pull request have been added to the analysis module conda environment.yml file.
• If applicable, R package dependencies required to run the code in this pull request have been added to the analysis module renv.lock file.

[sjspielman]

👍

[sjspielman]

seems like a good typo to fix!

[sjspielman]

Actually @allyhawkins how did you add rOpenScPCA? Did you snapshot, and if so, is there a file w/ library(rOpenScPCA) here?

[allyhawkins]

Actually @allyhawkins how did you add rOpenScPCA? Did you snapshot, and if so, is there a file w/ library(rOpenScPCA) here?

I did use renv::snapshot(). But I'm thinking that snapshot worked because I started using the package in the template notebook to prepare for the next PR/ to make sure it was working. I can add it to the dependencies.R file temporarily until that PR goes in.

[sjspielman]

But I'm thinking that snapshot worked because I started using the package in the template notebook to prepare for the next PR/ to make sure it was working. I can add it to the dependencies.R file temporarily until that PR goes in.

Makes sense, I don't think you need to add anything here. I have a lot of confidence it will be used soon!

[jaclyn-taroni]

Can you explain to me why we need this? It will be challenging to manage this under our current paradigm.

[allyhawkins]

Because I was getting an error running out of disk space when trying to build the image (see https://github.com/AlexsLemonade/OpenScPCA-analysis/actions/runs/11844604285).

I can see if I can make the image smaller?

[allyhawkins]

Or skip the test build for this module... but that seems not great.

[jaclyn-taroni]

I've made a change for now, but if we could make this smaller, that'd be swell. I prefer how we were handling permissions.