search

AlexsLemonade / OpenScPCA-analysis

An open, collaborative project to analyze data from the Single-cell Pediatric Cancer Atlas (ScPCA) Portal
Other
1 stars 8 forks source link

Update doublet Dockerfile #531

Closed sjspielman closed 1 week ago

sjspielman commented 1 week ago

Closes #460

This PR updates the Dockerfile in the doublet-detection module to use both R and python. This Dockerfile nearly builds, save some R package installation errors which may be problems on R's side (although both CRAN and bioconductor repos, so maybe not?). I'm going to keep playing around with this a bit, so opening as a draft.

Edit: building now! Let me know if I should go ahead and add a docker GHA here, too.

sjspielman commented 1 week ago

https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/531/commits/810522664e7b4e6ca253b76fd51ddb080aba7b5e is probably not needed, so will likely end up reverting but leaving for now just on the off chance...

jashapiro commented 1 week ago

Let me know if I should go ahead and add a docker GHA here, too.

Yeah, seems worth doing as long as you have a Dockerfile.

sjspielman commented 1 week ago

It's worth noting I created this file starting off docker_simulate-sce.yml - https://github.com/AlexsLemonade/OpenScPCA-analysis/blob/main/.github/workflows/docker_simulate-sce.yml. Do you want me to make parallel changes there too?

jashapiro commented 1 week ago

It's worth noting I created this file starting off docker_simulate-sce.yml - https://github.com/AlexsLemonade/OpenScPCA-analysis/blob/main/.github/workflows/docker_simulate-sce.yml. Do you want me to make parallel changes there too?

Yes, and I think we probably need to add the push block to the template action as well. I can't think of why I might have removed it there.

sjspielman commented 1 week ago

Looks like you already fixed the template file - it's just not in main yet! https://github.com/AlexsLemonade/OpenScPCA-analysis/blame/reproducibility-docs/templates/workflows/docker_module.yml

edit - Similarly, I got the docker_simulate-sce.yml from main too, and tags has been removed in reproducibility-docs already. So, I think we're good!