diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 48a56ff..01e5b45 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.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: ${{ runner.temp }}/package + + Upload-Docker: if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/newAnnotationGx' # needs: R-CMD-check diff --git a/Dockerfile b/Dockerfile index 9cdf140..8de4c03 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,7 +1,7 @@ # Build with: docker build -t bhklab/annotationgx-r:$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 @@ -9,10 +9,15 @@ 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 \ No newline at end of file diff --git a/vignettes/Cellosaurus.Rmd b/vignettes/Cellosaurus.Rmd index d7fc345..67f4e41 100644 --- a/vignettes/Cellosaurus.Rmd +++ b/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