Build Apptainer Images #70
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| name: Build Apptainer Images | |
| on: | |
| workflow_dispatch: | |
| workflow_run: | |
| workflows: ["Build container images for GHCR and Dockerhub"] | |
| types: | |
| - completed | |
| jobs: | |
| build-apptainer: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| base: | |
| - {image: 'ghcr.io/bioconductor/r-ver', outname: 'r-ver'} | |
| - {image: 'ghcr.io/bioconductor/bioconductor', outname: 'bioconductor'} | |
| - {image: 'ghcr.io/bioconductor/tidyverse', outname: 'tidyverse'} | |
| - {image: 'ghcr.io/bioconductor/shiny', outname: 'shiny'} | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Install Apptainer dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y \ | |
| autoconf \ | |
| automake \ | |
| cryptsetup \ | |
| fuse2fs \ | |
| git \ | |
| fuse \ | |
| libfuse-dev \ | |
| libseccomp-dev \ | |
| libtool \ | |
| pkg-config \ | |
| runc \ | |
| squashfs-tools \ | |
| squashfs-tools-ng \ | |
| uidmap \ | |
| wget \ | |
| zlib1g-dev \ | |
| libsubid-dev | |
| - name: Setup Go | |
| uses: actions/setup-go@v5 | |
| with: | |
| go-version: 1.24.1 | |
| - name: Install Apptainer | |
| run: | | |
| export VERSION=1.3.6 # Latest Apptainer version as of 2025-04 | |
| wget https://github.com/apptainer/apptainer/releases/download/v${VERSION}/apptainer-${VERSION}.tar.gz | |
| tar -xzf apptainer-${VERSION}.tar.gz | |
| cd apptainer-${VERSION} | |
| ./mconfig | |
| make -C ./builddir | |
| sudo make -C ./builddir install | |
| - name: Verify Apptainer config | |
| run: apptainer buildcfg | |
| - name: Get branch name | |
| id: vars | |
| shell: bash | |
| run: | | |
| BRANCH_NAME=${GITHUB_REF#refs/heads/} | |
| PROCESSED_NAME="$BRANCH_NAME" | |
| if [[ $BRANCH_NAME == RELEASE_* ]]; then | |
| PROCESSED_NAME=${BRANCH_NAME#RELEASE_} | |
| PROCESSED_NAME=${PROCESSED_NAME//_/.} | |
| fi | |
| echo "origbranch=$BRANCH_NAME" >> $GITHUB_OUTPUT | |
| echo "procbranch=$PROCESSED_NAME" >> $GITHUB_OUTPUT | |
| - name: Build Apptainer Image | |
| run: | | |
| apptainer build \ | |
| "${{matrix.base.outname}}-$(date +%s).sif" \ | |
| docker://${{ matrix.base.image }}:${{steps.vars.origbranch}} | |
| - name: Push to GitHub Packages | |
| run: | | |
| echo ${{ secrets.GITHUB_TOKEN }} | apptainer remote login -u ${{ github.actor }} --password-stdin oras://ghcr.io | |
| apptainer push *.sif oras://ghcr.io/${{github.repository_owner}}/${{matrix.base.outname}}:${{steps.vars.origbranch}} | |
| apptainer push *.sif oras://ghcr.io/${{github.repository_owner}}/${{matrix.base.outname}}:${{steps.vars.procbranch}} |