AlexsLemonade / AlexsLemonade/OpenScPCA-analysis

Keep tabs on Rhtslib installation in Dockerfiles

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OpenScPCA admin
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Forks
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Merged PRs (30d)
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Description

We have several modules (including `doublet-detection`, `cell-type-ewings`, and `cell-type-wilms-tumor-06`) whose Dockerfiles need are taking a separate step to install `Rhtslib` due to failures when it is installed using `renv`. This appears to be a problem on the Bioc/Rhtslib side, [not with `renv`](https://github.com/rstudio/renv/issues/1957).

The purpose of this issue is to keep tabs on that library installation for whether we can hopefully one day remove the extra line in the Dockerfiles installing it, and just let `renv` handle all the installs.

Contributor guide

Open the contributing guide

Research direction

Review the Dockerfiles for the `doublet-detection`, `cell-type-ewings`, and `cell-type-wilms-tumor-06` modules, and check whether `Rhtslib` still fails when installed through `renv`. Done means confirming that `renv` can handle the installation and removing the separate Dockerfile install step when that is reliable.

Written by the indexing model from the issue text.

Assessment

Tech stack
docker, dockerfile, r
Domain
devops
Issue type
Refactor
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
30/100

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