Fix logic for handling missing r2 values in vcf files #161
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| name: build | |
| on: | |
| push: | |
| branches: | |
| - main | |
| release: | |
| types: | |
| - published | |
| - edited | |
| jobs: | |
| build: | |
| runs-on: [self-hosted, ubuntu, x64] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| # Check out full history for `setuptools_scm` | |
| fetch-depth: 0 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| check-latest: true | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install \ | |
| awscli \ | |
| pygithub \ | |
| setuptools_scm | |
| - name: Set up metadata | |
| id: metadata | |
| shell: python | |
| run: | | |
| import os | |
| from github import Github | |
| from setuptools_scm import get_version | |
| pushed_at = "${{ github.event.repository.pushed_at }}" | |
| ref = "${{ github.ref }}" | |
| repository = "${{ github.repository }}" | |
| sha = "${{ github.sha }}" | |
| url = "${{ github.event.repository.html_url }}" | |
| registry = "${{ secrets.REGISTRY }}" | |
| token = "${{ secrets.GITHUB_TOKEN }}" | |
| repository_data = Github(token).get_repo(repository) | |
| repository_owner, repository_name = repository.lower().split("/") | |
| reference, type, name = ref.split("/")[:3] | |
| if reference != "refs": | |
| raise ValueError(f"Unknown reference: {reference}") | |
| if type == "heads": | |
| tag = {"main": "latest"}.get(name, name) | |
| push = True | |
| elif type == "tags": | |
| tag = name | |
| push = True | |
| else: | |
| raise ValueError(f"Unknown reference type: {type}") | |
| path = f"{registry}/{repository_name}" | |
| cache_from = f"type=registry,ref={path}:buildcache" | |
| output = dict( | |
| cache_from=cache_from, | |
| cache_to=f"{cache_from},compression=zstd,mode=max,image-manifest=true" if push else "", | |
| labels=[ | |
| f'org.opencontainers.image.created="{pushed_at}"', | |
| 'org.opencontainers.image.authors="Lea Waller <[email protected]>"', | |
| f'org.opencontainers.image.url="{url}"', | |
| f'org.opencontainers.image.documentation="{url}"', | |
| f'org.opencontainers.image.source="{url}"', | |
| f'org.opencontainers.image.version="{get_version()}"', | |
| f'org.opencontainers.image.revision="{sha}"', | |
| f'org.opencontainers.image.licenses="{repository_data.license.spdx_id}"', | |
| f'org.opencontainers.image.title="{repository_name}"', | |
| f'org.opencontainers.image.description="{repository_data.description}"', | |
| ], | |
| push=str(push).lower(), | |
| build_tag=f"{repository_name}:{tag}", | |
| push_tags=[ | |
| f"{path}:{tag}", | |
| f"docker.io/{repository_owner}/{repository_name}:{tag}", | |
| ] | |
| if push | |
| else [], | |
| singularity_name=f"{repository_name}-{tag}.sif", | |
| ) | |
| with open(os.environ["GITHUB_OUTPUT"], "at") as file_handle: | |
| for key, value in output.items(): | |
| if isinstance(value, list): | |
| file_handle.write("\n".join([f"{key}<<eof", *value, "eof"]) + "\n") | |
| else: | |
| file_handle.write(f"{key}={value}\n") | |
| - name: Login to DockerHub | |
| uses: docker/login-action@v3 | |
| if: ${{ steps.metadata.outputs.push == 'true' }} | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Login to container registry | |
| uses: docker/login-action@v3 | |
| if: ${{ steps.metadata.outputs.push == 'true' }} | |
| with: | |
| registry: ${{ secrets.REGISTRY }} | |
| username: ${{ secrets.REGISTRY_USERNAME }} | |
| password: ${{ secrets.REGISTRY_PASSWORD }} | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Build container | |
| uses: docker/build-push-action@v6 | |
| with: | |
| cache-from: ${{ steps.metadata.outputs.cache_from }} | |
| cache-to: ${{ steps.metadata.outputs.cache_to }} | |
| context: "." | |
| file: "./Dockerfile" | |
| labels: | | |
| ${{ steps.metadata.outputs.labels }} | |
| load: true | |
| platforms: linux/amd64 | |
| push: false | |
| tags: | | |
| ${{ steps.metadata.outputs.build_tag }} | |
| - name: Push container to registry | |
| if: ${{ steps.metadata.outputs.push == 'true' }} | |
| uses: docker/build-push-action@v6 | |
| with: | |
| cache-from: ${{ steps.metadata.outputs.cache_from }} | |
| context: "." | |
| file: "./Dockerfile" | |
| labels: | | |
| ${{ steps.metadata.outputs.labels }} | |
| platforms: linux/amd64 | |
| push: true | |
| tags: | | |
| ${{ steps.metadata.outputs.push_tags }} | |
| - name: Set up Apptainer | |
| run: | | |
| sudo add-apt-repository --yes "ppa:apptainer/ppa" | |
| sudo apt install --yes "apptainer" | |
| - name: Build Apptainer container | |
| if: ${{ steps.metadata.outputs.push == 'true' }} | |
| env: | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| AWS_ENDPOINT_URL: ${{ secrets.AWS_ENDPOINT_URL }} | |
| run: | | |
| mkdir "singularity" | |
| apptainer build \ | |
| --disable-cache \ | |
| "./singularity/${{ steps.metadata.outputs.singularity_name }}" \ | |
| "docker-daemon://${{ steps.metadata.outputs.build_tag }}" | |
| image_file=$(find "./singularity" -type f | head --lines=1) | |
| # Check if the container works | |
| apptainer exec "${image_file}" score --help | |
| # Upload the container | |
| aws s3 mv \ | |
| --acl public-read \ | |
| "${image_file}" \ | |
| "s3://download-gwas-science/singularity/" | |
| - name: Build Singularity 2.x container | |
| if: ${{ steps.metadata.outputs.push == 'true' }} | |
| env: | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| AWS_ENDPOINT_URL: ${{ secrets.AWS_ENDPOINT_URL }} | |
| run: | | |
| mkdir "singularity-2" | |
| docker run \ | |
| --privileged \ | |
| --rm \ | |
| --volume="/var/run/docker.sock:/var/run/docker.sock" \ | |
| --volume="./singularity-2:/output" \ | |
| "quay.io/singularity/docker2singularity:v2.6" \ | |
| --name "${{ steps.metadata.outputs.singularity_name }}" \ | |
| "${{ steps.metadata.outputs.build_tag }}" | |
| image_file=$(find "./singularity-2" -type f | head --lines=1) | |
| # Check if the container works | |
| apptainer exec "${image_file}" score --help | |
| # Upload the container | |
| aws s3 mv \ | |
| --acl public-read \ | |
| "${image_file}" \ | |
| "s3://download-gwas-science/singularity/" |