ci: add Dockerfile & gha for building container automatically

.github/workflows/docker.yml

@@ -0,0 +1,59 @@
+name: docker
+
+on:
+  workflow_dispatch:
+  release:
+    types: [published]
+
+env:
+  IMAGE_NAME: "scworkflow" # must be lowercase
+  CONTEXT: "./"
+  NAMESPACE: "nciccbr"
+
+permissions: read-all
+
+jobs:
+  build-docker:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Prepare build-time variables
+        id: vars
+        run: |
+          echo "DATE=$(date +"%Y-%m-%d")" >> "$GITHUB_OUTPUT"
+
+          if [ '${{ github.event_name }}' == 'release' ]; then
+            VERSION=${{ github.ref_name }}
+            DOCKER_TAGS=${{ env.NAMESPACE }}/${{ env.IMAGE_NAME }}:${VERSION},${{ env.NAMESPACE }}/${{ env.IMAGE_NAME }}:latest
+          else
+            HASH=$(git rev-parse --short HEAD)
+            VERSION="$(grep 'Version:' $CONTEXT/DESCRIPTION | sed 's/Version: /v/')_${HASH}"
+            DOCKER_TAGS=${{ env.NAMESPACE }}/${{ env.IMAGE_NAME }}:${VERSION}
+          fi
+          echo "VERSION_TAG=$(echo $VERSION)" >> "$GITHUB_OUTPUT"
+          echo "DOCKER_TAGS=$(echo $DOCKER_TAGS)" >> "$GITHUB_OUTPUT"
+
+      - name: debug
+        run: |
+          echo "the github tag is ${{ github.ref_name }}"
+          echo "github event_name is ${{ github.event_name }}"
+          echo "the version tag is ${{ steps.vars.outputs.VERSION_TAG }}"
+
+      - name: Login to DockerHub
+        if: ${{ github.event_name != 'pull_request' }}
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      - name: Build and push
+        uses: docker/build-push-action@v4
+        with:
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.vars.outputs.DOCKER_TAGS }} # include 'latest' tag if this is a release
+          context: ${{ env.CONTEXT }}
+          file: ${{ env.CONTEXT }}/Dockerfile
+          build-args: |
+            BUILD_DATE=${{ steps.vars.outputs.DATE }}
+            BUILD_TAG=${{ steps.vars.outputs.VERSION_TAG }}
+            REPONAME=${{ env.IMAGE_NAME }}
+            R_VERSION=4.3.2

Dockerfile

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+FROM nciccbr/ccbr_ubuntu_22.04:v4
+
+# build time variables
+ARG BUILD_DATE="000000"
+ENV BUILD_DATE=${BUILD_DATE}
+ARG BUILD_TAG="000000"
+ENV BUILD_TAG=${BUILD_TAG}
+ARG REPONAME="000000"
+ENV REPONAME=${REPONAME}
+
+ARG R_VERSION=4.3.2
+ENV R_VERSION=${R_VERSION}
+
+SHELL ["/bin/bash", "-lc"]
+
+# Install conda and give write permissions to conda folder
+RUN echo 'export PATH=/opt2/conda/bin:$PATH' > /etc/profile.d/conda.sh && \
+    wget --quiet "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" -O ~/miniforge3.sh && \
+    /bin/bash ~/miniforge3.sh -b -p /opt2/conda && \
+    rm ~/miniforge3.sh && chmod 777 -R /opt2/conda/
+ENV PATH="/opt2/conda/bin:$PATH"
+
+# Pin channels and update
+RUN conda config --add channels conda-forge \
+ && conda config --add channels bioconda \
+ && conda config --set channel_priority strict
+
+# install conda packages
+RUN mamba install -y -c conda-forge \
+    r-base=${R_VERSION} \
+    r-devtools \
+    r-ggplot2 \
+    r-ggrepel r-viridis r-upsetr r-patchwork r-plotly \
+    r-matrix r-mgcv r-survival \
+    bioconductor-genomicranges \
+    bioconductor-summarizedexperiment \
+    bioconductor-delayedarray \
+    bioconductor-s4arrays \
+    bioconductor-annotationdbi \
+    bioconductor-annotate \
+    bioconductor-keggrest \
+  && conda clean -afy
+
+# install R package
+COPY . /opt2/SCWorkflow
+RUN R -e "devtools::install_local('/opt2/SCWorkflow', dependencies = TRUE, repos='http://cran.rstudio.com')"
+
+# add scworkflow exec to the path
+# RUN chmod -R +x /opt2/conda/lib/R/library/SCWorkflow/exec
+# ENV PATH="$PATH:/opt2/conda/lib/R/library/SCWorkflow/exec"
+# RUN scworkflow --help
+
+# copy example script & json to data
+COPY ./inst/extdata/example_script.sh /data2/
+COPY ./inst/extdata/json_args/ /data2/json_args/
+
+# Save Dockerfile in the docker
+COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+RUN chmod a+r /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+
+# cleanup
+WORKDIR /data2
+RUN apt-get clean && apt-get purge \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*