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Add rOpenScPCA to renv/docker in ewing module #881

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merged 4 commits into from
Nov 15, 2024
Merged

Add rOpenScPCA to renv/docker in ewing module #881

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24ec90b
add rOpenScPCA to lock file
allyhawkins Nov 14, 2024
c356c2a
fix typo on GHA
allyhawkins Nov 14, 2024
79fba34
Merge branch 'main' into allyhawkins/ewings-add-ropenscpca-to-docker
allyhawkins Nov 14, 2024
e791f26
use larger runner for test build
allyhawkins Nov 14, 2024
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4 changes: 2 additions & 2 deletions .github/workflows/docker_cell-type-ewings.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ jobs:
test-build:
name: Test Build Docker Image
if: github.event_name == 'pull_request' || (contains(github.event_name, 'workflow_') && !inputs.push-ecr)
runs-on: ubuntu-latest
runs-on: openscpca-22.04-big-disk
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Can you explain to me why we need this? It will be challenging to manage this under our current paradigm.

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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?

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

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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.


steps:
- name: Set up Docker Buildx
Expand All @@ -49,7 +49,7 @@ jobs:
- name: Build image
uses: docker/build-push-action@v6
with:
context: "{{defaultContext}}:analyses/simulate-sce"
context: "{{defaultContext}}:analyses/cell-type-ewings"
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seems like a good typo to fix!

push: false
cache-from: type=gha
cache-to: type=gha,mode=max
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25 changes: 24 additions & 1 deletion analyses/cell-type-ewings/renv.lock
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Expand Up @@ -3843,6 +3843,29 @@
],
"Hash": "16f095487215acf101cdc3ed3da237cf"
},
"rOpenScPCA": {
"Package": "rOpenScPCA",
"Version": "0.1.0",
"Source": "GitHub",
"RemoteType": "github",
"RemoteHost": "api.github.com",
"RemoteUsername": "AlexsLemonade",
"RemoteRepo": "rOpenScPCA",
"RemoteRef": "main",
"RemoteSha": "fe1cf9f9ad016a1e9724a6274e88a5b841455bf5",
"Requirements": [
"BiocParallel",
"SingleCellExperiment",
"bluster",
"dplyr",
"methods",
"pdfCluster",
"purrr",
"tibble",
"tidyr"
],
"Hash": "b6805f308a847b08322572b63da51a4d"
},
"rappdirs": {
"Package": "rappdirs",
"Version": "0.3.3",
Expand Down Expand Up @@ -4173,8 +4196,8 @@
"Package": "scpcaTools",
"Version": "0.3.2",
"Source": "GitHub",
"Remotes": "AlexsLemonade/scpcaData, immunogenomics/[email protected]",
"RemoteType": "github",
"Remotes": "AlexsLemonade/scpcaData, immunogenomics/[email protected]",
"RemoteHost": "api.github.com",
"RemoteRepo": "scpcaTools",
"RemoteUsername": "AlexsLemonade",
Expand Down