Missing tools/packages to Python3/R containers (#281) #20
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| # action to build and push the gwas Docker and Singularity image at each tag (for release) | |
| name: build & push gwas Docker image | |
| on: | |
| push: | |
| tags: | |
| - "v*.*.*" | |
| env: | |
| LATEST_TAG: ghcr.io/comorment/gwas:latest | |
| jobs: | |
| docker: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - | |
| name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| lfs: 'true' | |
| sparse-checkout: | | |
| test-requirements.txt | |
| tests | |
| - | |
| name: Docker meta | |
| id: meta | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: | | |
| ghcr.io/${{ github.repository_owner }}/gwas | |
| tags: | | |
| type=ref,event=branch | |
| type=semver,pattern={{version}} | |
| type=sha | |
| type=raw,value=latest,enable={{is_default_branch}} | |
| - | |
| name: Set up QEMU | |
| uses: docker/setup-qemu-action@v3 | |
| - | |
| name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - | |
| name: Login to GitHub Container Registry | |
| if: github.event_name != 'pull_request' | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - | |
| name: Build and export to Docker | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: "{{defaultContext}}:docker" | |
| load: true | |
| tags: ${{ env.LATEST_TAG }} | |
| file: | |
| ./dockerfiles/gwas/Dockerfile | |
| - | |
| name: Test | |
| run: | | |
| git lfs pull -I tests/extras/*.tar.gz | |
| pip3 install -r test-requirements.txt | |
| py.test -v tests/test_gwas.py | |
| - | |
| name: Build and push | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: "{{defaultContext}}:docker" | |
| push: ${{ github.event_name != 'pull_request' }} | |
| tags: ${{ steps.meta.outputs.tags }} | |
| file: | |
| ./dockerfiles/gwas/Dockerfile | |
| platforms: linux/amd64 | |
| build-apptainer-container: | |
| needs: docker | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| packages: write | |
| name: Build Apptainer Container | |
| steps: | |
| - name: Check out code for the container builds | |
| uses: actions/checkout@v4 | |
| - name: Docker meta | |
| id: meta | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: | | |
| ghcr.io/${{ github.repository_owner }}/gwas | |
| tags: | | |
| type=semver,pattern={{version}} | |
| type=ref,event=branch | |
| type=sha | |
| type=raw,value=latest,enable={{is_default_branch}} | |
| - name: Build and push Apptainer container | |
| run: | | |
| tags="${{ steps.meta.outputs.tags }}" | |
| csv_tags=$(printf "%s\n" "$tags" | awk -F: 'NR==1{printf "%s,", $0; next} {printf "%s,", $NF}' | sed 's/,$//') | |
| IFS= read -r first_tag <<EOF | |
| $tags | |
| EOF | |
| push_tags="$(printf $csv_tags | sed -e "s/gwas/gwas_sif/g")" | |
| echo ${{ secrets.GITHUB_TOKEN }} | oras login --username ${{ github.repository_owner }} --password-stdin ghcr.io | |
| docker pull kaczmarj/apptainer:latest | |
| docker run --rm --privileged -v $(pwd):/work kaczmarj/apptainer build gwas.sif docker://"$first_tag" | |
| oras push "$push_tags" --artifact-type application/vnd.acme.rocket.config gwas.sif | |
| rm gwas.sif | |
| shell: sh |