Ensure that R packages geneplotter and RColorBrewer are available #131
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| name: build | |
| on: | |
| push: | |
| branches: | |
| - main | |
| release: | |
| types: | |
| - published | |
| - edited | |
| jobs: | |
| docker_build: | |
| runs-on: self-hosted | |
| outputs: | |
| tag: ${{ steps.build_tag.outputs.tag }} | |
| steps: | |
| - name: Login to DockerHub | |
| uses: docker/login-action@v3 | |
| with: | |
| username: hippocampusgirl | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Login to container registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ secrets.REGISTRY }} | |
| username: ${{ secrets.REGISTRY_USERNAME }} | |
| password: ${{ secrets.REGISTRY_PASSWORD }} | |
| - name: Set up build tag | |
| id: build_tag | |
| shell: bash | |
| env: | |
| github_ref: ${{ github.ref }} | |
| github_repository: ${{ github.repository }} | |
| run: | | |
| version=$(echo "${github_ref}" | cut -d '/' -f 3) | |
| if [[ "$version" == "main" ]]; then | |
| version=latest | |
| fi | |
| owner=$( \ | |
| echo "${github_repository}" | \ | |
| cut -d'/' -f1 | \ | |
| tr '[:upper:]' '[:lower:]' \ | |
| ) | |
| name=$( \ | |
| echo "${github_repository}" | \ | |
| cut -d'/' -f2 | \ | |
| sed -r 's/([A-Za-z0-9])([A-Z])([a-z0-9])/\1-\L\2\3/g' | \ | |
| tr '[:upper:]' '[:lower:]' \ | |
| ) | |
| echo "repo=${name}" >> ${GITHUB_OUTPUT} | |
| echo "tag=${name}:${version}" >> ${GITHUB_OUTPUT} | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Build and push to container registry | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: "." | |
| file: "./Dockerfile" | |
| platforms: linux/amd64 | |
| cache-from: type=registry,ref=${{ secrets.REGISTRY }}/${{ steps.build_tag.outputs.repo }}:buildcache | |
| cache-to: type=registry,ref=${{ secrets.REGISTRY }}/${{ steps.build_tag.outputs.repo }}:buildcache,compression=zstd,mode=max | |
| outputs: type=image,name=${{ secrets.REGISTRY }}/${{ steps.build_tag.outputs.tag }},push=true,compression=gzip,compression-level=9,force-compression=true | |
| labels: | | |
| org.opencontainers.image.title=${{ github.event.repository.name }} | |
| org.opencontainers.image.url=${{ github.event.repository.html_url }} | |
| org.opencontainers.image.source=${{ github.event.repository.html_url }} | |
| org.opencontainers.image.revision=${{ github.sha }} | |
| org.opencontainers.image.created=${{ github.event.repository.updated_at}} | |
| singularity_build: | |
| runs-on: self-hosted | |
| needs: | |
| - docker_build | |
| defaults: | |
| run: | |
| shell: bash --login -x -e {0} | |
| steps: | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| auto-activate-base: true | |
| activate-environment: "" | |
| use-mamba: true | |
| - name: Set up Singularity | |
| run: | | |
| mamba install --yes singularity | |
| - name: Singularity build | |
| id: singularity_build | |
| env: | |
| docker_build_tag: ${{ needs.docker_build.outputs.tag }} | |
| run: | | |
| # Configure Singularity to not use the host's /tmp folder | |
| # because it is too small | |
| export SINGULARITY_TMPDIR="${PWD}" | |
| # Build Singularity image from Docker image | |
| singularity_build_name=$(echo -n ${docker_build_tag} | tr -c '[:alnum:]' '-') | |
| singularity build --disable-cache \ | |
| ${singularity_build_name}.sif \ | |
| docker://${{ secrets.REGISTRY }}/${docker_build_tag} | |
| echo "name=${singularity_build_name}" >> ${GITHUB_OUTPUT} | |
| - name: Upload to DigitalOcean | |
| env: | |
| digitalocean_access_key: ${{ secrets.DIGITALOCEAN_ACCESS_KEY }} | |
| digitalocean_secret_key: ${{ secrets.DIGITALOCEAN_SECRET_KEY }} | |
| digitalocean_region: ${{ secrets.DIGITALOCEAN_REGION }} | |
| digitalocean_space_name: ${{ secrets.DIGITALOCEAN_SPACE_NAME }} | |
| singularity_build_name: ${{ steps.singularity_build.outputs.name }} | |
| run: | | |
| pip install s3cmd | |
| s3cmd --stop-on-error \ | |
| --ssl --no-encrypt \ | |
| --access_key="${digitalocean_access_key}" \ | |
| --secret_key="${digitalocean_secret_key}" \ | |
| --host="${digitalocean_region}.digitaloceanspaces.com" \ | |
| --host-bucket="%(bucket)s.${digitalocean_region}.digitaloceanspaces.com" \ | |
| --dump-config \ | |
| > ${HOME}/.s3cfg | |
| s3cmd put ${singularity_build_name}.sif s3://${digitalocean_space_name}/singularity/ | |
| s3cmd setacl s3://${digitalocean_space_name}/singularity/${singularity_build_name}.sif --acl-public |