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Merge pull request #17 from c3g/genpipesV
Consolidation + removing dev GenPipes as GenPipes 5 is a package
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| singularity/ | ||
| container/ |
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| name: Create and publish a Docker image | ||
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| # Configures this workflow to run every time a change is pushed to the branch called 'main' or a PR is opened on 'main. | ||
| on: | ||
| push: | ||
| branches: ['main'] | ||
| release: | ||
| types: [published] | ||
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| # Defines two custom environment variables for the workflow. These are used for the Container registry domain, and a name for the Docker image that this workflow builds. | ||
| env: | ||
| REGISTRY: ghcr.io | ||
| IMAGE_NAME: ${{ github.repository }} | ||
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| # There is a single job in this workflow. It's configured to run on the latest available version of Ubuntu. | ||
| jobs: | ||
| build-and-push-docker: | ||
| runs-on: ubuntu-latest | ||
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| # Sets the permissions granted to the `GITHUB_TOKEN` for the actions in this job. | ||
| permissions: | ||
| contents: read | ||
| packages: write | ||
| attestations: write | ||
| id-token: write | ||
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| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v4 | ||
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| - name: Set up QEMU | ||
| uses: docker/setup-qemu-action@v3 | ||
| with: | ||
| platforms: linux/amd64,linux/arm64 | ||
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| - name: Set up Docker Buildx | ||
| uses: docker/setup-buildx-action@v3 | ||
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| # Uses the `docker/login-action` action to log in to the Container registry using the account and password that will publish the packages. | ||
| # Once published, the packages are scoped to the account defined here. | ||
| - name: Log in to the Container registry | ||
| uses: docker/login-action@v3 | ||
| with: | ||
| registry: ${{ env.REGISTRY }} | ||
| username: ${{ github.actor }} | ||
| password: ${{ secrets.GITHUB_TOKEN }} | ||
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| # This step uses [docker/metadata-action](https://github.com/docker/metadata-action#about) to extract tags and labels that will be applied to the specified image. | ||
| # The `id` "meta" allows the output of this step to be referenced in a subsequent step. The `images` value provides the base name for the tags and labels. | ||
| - name: Extract metadata (tags, labels) for Docker | ||
| id: meta | ||
| uses: docker/metadata-action@v5 | ||
| with: | ||
| images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} | ||
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| # This step uses the `docker/build-push-action` action to build the image, based on your repository's `Dockerfile`. | ||
| # If the build succeeds, it pushes the image to GitHub Packages. | ||
| # It uses the `context` parameter to define the build's context as the set of files located in the specified path. | ||
| # For more information, see "[Usage](https://github.com/docker/build-push-action#usage)" in the README of the `docker/build-push-action` repository. | ||
| # It uses the `tags` and `labels` parameters to tag and label the image with the output from the "meta" step. | ||
| - name: Build and push Docker image | ||
| id: push | ||
| uses: docker/build-push-action@v6 | ||
| with: | ||
| platforms: linux/amd64,linux/arm64 | ||
| context: . | ||
| push: true | ||
| tags: ${{ steps.meta.outputs.tags }} | ||
| labels: ${{ steps.meta.outputs.labels }} | ||
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| # This step generates an artifact attestation for the image, which is an unforgeable statement about where and how it was built. | ||
| # It increases supply chain security for people who consume the image. | ||
| # For more information, see "[AUTOTITLE](/actions/security-guides/using-artifact-attestations-to-establish-provenance-for-builds)." | ||
| - name: Generate artifact attestation | ||
| uses: actions/attest-build-provenance@v1 | ||
| with: | ||
| subject-name: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME}} | ||
| subject-digest: ${{ steps.push.outputs.digest }} | ||
| push-to-registry: true | ||
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| build-and-push-apptainer: | ||
| runs-on: ubuntu-latest | ||
| if: ${{ ! startsWith(github.ref, 'refs/tags/') }} | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - uses: eWaterCycle/setup-apptainer@v2 | ||
| with: | ||
| apptainer-version: 1.3.4 | ||
| - name: Create sif image | ||
| run: | | ||
| apptainer build -F container/wrapper_genpipes/images/genpipes-${{ env.TAG_NAME }}.sif docker://${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ env.TAG_NAME }} | ||
| cd container/wrapper_genpipes/images/ | ||
| ln -sf genpipes-${{ env.TAG_NAME }}.sif genpipes.sif | ||
| cd ../../ | ||
| tar -zcvf wrapper_genpipes.tgz wrapper_genpipes | ||
| - name: Upload sif image | ||
| uses: svenstaro/upload-release-action@v2 | ||
| with: | ||
| repo_token: ${{ secrets.GITHUB_TOKEN }} | ||
| file: container/wrapper_genpipes.tgz | ||
| asset_name: wrapper_genpipes.tgz | ||
| tag: ${{ github.ref }} | ||
| overwrite: true |
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| cvmfschecksum.* | ||
| *_mount_cache.sh | ||
| singularity/wrapper_genpipes/images | ||
| singularity/wrapper_genpipes.tgz | ||
| container/wrapper_genpipes/images | ||
| container/wrapper_genpipes.tgz | ||
| .DS_Store |
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| FROM centos:7.9.2009 | ||
| MAINTAINER P-O Quirion [email protected] | ||
| FROM ubuntu:24.04 | ||
| LABEL authors="P-O Quirion [email protected], Paul Stretenowich [email protected]" | ||
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| WORKDIR /tmp | ||
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| # All yum cmd | ||
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| ENV CVMFS_VERSION latest | ||
| ENV CC_STACK latest | ||
| ENV MODULE_VERSION 4.1.2 | ||
| RUN yum install -y https://ecsft.cern.ch/dist/cvmfs/cvmfs-release/cvmfs-release-${CVMFS_VERSION}.noarch.rpm \ | ||
| https://package.computecanada.ca/yum/cc-cvmfs-public/prod/RPM/computecanada-release-${CC_STACK}.noarch.rpm | ||
| RUN yum update -y \ | ||
| && yum install -y ImageMagick pigz which wget zip unzip.x86_64 make.x86_64 gcc expectk file \ | ||
| dejagnu less tcl-devel.x86_64 cvmfs-config-computecanada \ | ||
| cvmfs-fuse3 cvmfs-config-default \ | ||
| && yum clean all | ||
| ENV CVMFS_VERSION=latest | ||
| ENV CC_STACK=latest | ||
| ENV MODULE_VERSION=4.1.2 | ||
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| # All apt-get cmd | ||
| RUN apt-get update -y && \ | ||
| apt-get install -y wget lsb-release && \ | ||
| wget https://ecsft.cern.ch/dist/cvmfs/cvmfs-release/cvmfs-release-${CVMFS_VERSION}_all.deb && \ | ||
| dpkg -i cvmfs-release-${CVMFS_VERSION}_all.deb && \ | ||
| rm -f cvmfs-release-${CVMFS_VERSION}_all.deb && \ | ||
| apt-get update -y && \ | ||
| apt-get install -y cvmfs && \ | ||
| wget https://package.computecanada.ca/yum/cc-cvmfs-public/prod/other/cvmfs-config-computecanada-${CC_STACK}.all.deb && \ | ||
| apt-get install -y ./cvmfs-config-computecanada-${CC_STACK}.all.deb && \ | ||
| rm -f cvmfs-config-computecanada-${CC_STACK}.all.deb && \ | ||
| apt-get install -y libpng-dev libjpeg-dev libtiff-dev && \ | ||
| apt-get install -y imagemagick pigz which zip unzip make gcc expect file dejagnu less tcl-dev cvmfs-config-computecanada cvmfs-fuse3 cvmfs-config-default && \ | ||
| apt-get clean all | ||
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| RUN mkdir /cvmfs-cache && chmod 777 /cvmfs-cache /cvmfs | ||
| RUN mkdir /cvmfs/ref.mugqic /cvmfs/soft.mugqic /cvmfs/cvmfs-config.computecanada.ca | ||
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| # module | ||
| RUN wget https://github.com/cea-hpc/modules/releases/download/v${MODULE_VERSION}/modules-${MODULE_VERSION}.tar.gz | ||
| RUN tar xzf modules-${MODULE_VERSION}.tar.gz && \ | ||
| RUN wget https://github.com/cea-hpc/modules/releases/download/v${MODULE_VERSION}/modules-${MODULE_VERSION}.tar.gz && \ | ||
| tar xzf modules-${MODULE_VERSION}.tar.gz && \ | ||
| rm modules-${MODULE_VERSION}.tar.gz \ | ||
| && cd modules-${MODULE_VERSION} && ./configure && make -j 7 && make install \ | ||
| && cd .. && rm -rf modules-${MODULE_VERSION} && rm -rf /usr/local/Modules/modulefiles/* | ||
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| # CVMFS | ||
| ADD default.local /etc/cvmfs/default.local | ||
| ADD soft.mugqic.local /etc/cvmfs/config.d/soft.mugqic.local | ||
| ADD ref.mugqic.local /etc/cvmfs/config.d/ref.mugqic.local | ||
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| RUN ["ln", "-s", "/usr/local/Modules/init/profile.sh", "/etc/profile.d/z00_module.sh"] | ||
| RUN echo "source /etc/profile.d/z00_module.sh" >> /etc/bashrc | ||
| ADD devmodule/genpipes "/usr/local/Modules/modulefiles/." | ||
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| ADD genpipesrc /usr/local/etc/genpiperc | ||
| ADD genpipesrc /usr/local/etc/genpiperc | ||
| RUN ["ln", "-s", "/usr/local/etc/genpiperc", "/etc/profile.d/z90_genpipes.sh"] | ||
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| ADD init_genpipes /usr/local/bin/init_genpipes | ||
| RUN chmod 755 /usr/local/bin/init_genpipes | ||
| ENTRYPOINT ["init_genpipes"] | ||
| #docker build --tag c3genomics/genpipes:alpha -f Dockerfile . && singularity build -F ../genpipes_alpha.sif docker-daemon://c3genomics/genpipes:alpha |
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