Add GHCR Docker image build/publish workflow for HPCell

.Rbuildignore

@@ -12,4 +12,6 @@ pipeline_stores
 ^[^/]*\.r$
 ^tests$
 _targets
-target_framework
+target_framework
+^Dockerfile$
+^\\.dockerignore$

.dockerignore

@@ -0,0 +1,7 @@
+.git
+.github
+.Rproj.user
+renv
+renv.lock
+pipeline_store
+_targets

.github/workflows/docker-image.yml

@@ -0,0 +1,56 @@
+name: docker-image
+
+on:
+  push:
+    branches:
+      - main
+      - master
+    tags:
+      - 'v*'
+  pull_request:
+    branches:
+      - main
+      - master
+  workflow_dispatch:
+
+jobs:
+  build-and-publish:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to GitHub Container Registry
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ghcr.io/${{ github.repository_owner }}/hpcell
+          tags: |
+            type=ref,event=branch
+            type=ref,event=pr
+            type=semver,pattern={{version}}
+            type=sha
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: ./Dockerfile
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

Dockerfile

@@ -0,0 +1,8 @@
+FROM ghcr.io/bioconductor/bioconductor_docker:RELEASE_3_21
+
+COPY . /opt/HPCell
+RUN R -q -e "desc <- read.dcf('/opt/HPCell/DESCRIPTION'); pkgs <- unique(trimws(unlist(strsplit(paste(desc[1, c('Depends', 'Imports')], collapse = ','), ',')))); pkgs <- sub('\\\\s*\\\\(.*\\\\)', '', pkgs); pkgs <- pkgs[pkgs != '' & pkgs != 'R']; repos <- c(CRAN = 'https://cloud.r-project.org', BioCsoft = 'https://bioconductor.org/packages/3.21/bioc', BioCann = 'https://bioconductor.org/packages/3.21/data/annotation', BioCexp = 'https://bioconductor.org/packages/3.21/data/experiment', BioCworkflows = 'https://bioconductor.org/packages/3.21/workflows'); install.packages(pkgs, repos = repos)"
+RUN R CMD INSTALL /opt/HPCell
+
+WORKDIR /work
+CMD ["R"]

README.md

@@ -53,6 +53,15 @@ The key features of HPCell include:
 remotes::install_github("MangiolaLaboratory/HPCell")
 ```
 
+### Docker image
+
+GitHub Actions now publishes a pre-built container image to GHCR:
+
+``` bash
+docker pull ghcr.io/mangiolalaboratory/hpcell:main
+docker run --rm -it ghcr.io/mangiolalaboratory/hpcell:main
+```
+
 ## The input
 
 The pipeline accepts a vector of file paths. If this vector is named,

README.rmd

@@ -39,6 +39,15 @@ remotes::install_github("MangiolaLaboratory/HPCell")
 
 ```
 
+### Docker image
+
+GitHub Actions now publishes a pre-built container image to GHCR:
+
+```{bash, eval=FALSE}
+docker pull ghcr.io/mangiolalaboratory/hpcell:main
+docker run --rm -it ghcr.io/mangiolalaboratory/hpcell:main
+```
+
 ## The input
 
 The pipeline accepts a vector of file paths.
@@ -724,4 +733,3 @@ By summarizing single-cell data into groups, it mimics traditional bulk RNA-seq
 ... |> 
   tidySingleCellExperiment::aggregate_cells(!!x, slot = "data", assays=assays) 
 ```
-