Add Docker build and test workflow***

***Update Dockerfile to use bioconductor/bioconductor:3.17***
***Update vignettes with example pipeline

.github/workflows/R-CMD-check.yaml

@@ -45,6 +45,34 @@ jobs:
         with:
           upload-snapshots: true
 
+  Test-Docker-Build:
+    # needs: R-CMD-check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      - name: Get TAG from DESCRIPTION
+        run: |
+          TAG=$(grep  'Version:' DESCRIPTION  | grep -oE '[0-9]+(\.[0-9]+)*')
+          echo "TAG=$TAG" >> $GITHUB_ENV
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Test Docker Build
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          platforms: linux/amd64,linux/arm64
+          file: ./Dockerfile
+          push: false
+
   Code-Coverage:
     runs-on: ubuntu-latest
     env:
@@ -86,6 +114,8 @@ jobs:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package
 
+
+
   Upload-Docker:
     if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/newAnnotationGx'
     # needs: R-CMD-check

Dockerfile

@@ -1,18 +1,23 @@
 # Build with: docker build -t bhklab/annotationgx-r:$TAG -f Dockerfile .
 #  you can set TAG=$(grep  'Version:' DESCRIPTION  | grep -oE '[0-9]+(\.[0-9]+)*')
 # To push to dockerhub run docker push bhklab/annotationgx-r:$TAG
-FROM rocker/r-base
+FROM bioconductor/bioconductor:3.17
 
 # copy the current directory contents into the container at /app
 COPY . /app
 
 # set a working directory
 WORKDIR /app
 
-RUN apt-get -qq update && \
-  apt-get install -y --no-install-recommends git libxml2-dev
+RUN R -e 'devtools::install_github("bhklab/AnnotationGx", upgrade = T)'
 
-RUN Rscript -e "install.packages('pak', repos = 'https://r-lib.github.io/p/pak/dev/')"
-RUN Rscript -e "pak::pkg_install(c('jsonlite','bhklab/AnnotationGx@main'), ask = F)"
+# RUN install2.r --error --deps TRUE \
+#     qpdf \
+#     devtools \
+#     jsonlite \
+#     && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
 
+# RUN apt-get clean && apt-get -y update && apt-get install -y --no-install-recommends curl
 
+# RUN installGithub.r \
+#     bhklab/AnnotationGx

vignettes/Cellosaurus.Rmd

@@ -108,7 +108,7 @@ mapCell2Accession("BT474", numResults=1, prioritizeParent=TRUE)
 
 
 
-### Example pipeline to annotate a dataset
+### Example pipeline to annotate a dataseGSM1897356t
 #TODO::incomplete
 
 We will be working with some data from the GDSC and Cell Model Passports datasets