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Consolidation + removing dev GenPipes as GenPipes 5 is a package
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| @@ -1 +1 @@ | ||
| 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'] | ||
| pull_request: | ||
| branches: ['main'] | ||
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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 }} | ||
|
|
||
| # There is a single job in this workflow. It's configured to run on the latest available version of Ubuntu. | ||
| jobs: | ||
| build-and-push-image: | ||
| runs-on: ubuntu-latest | ||
|
|
||
| # 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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| # 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@65b78e6e13532edd9afa3aa52ac7964289d1a9c1 | ||
| with: | ||
| registry: ${{ env.REGISTRY }} | ||
| username: ${{ github.actor }} | ||
| password: ${{ secrets.GITHUB_TOKEN }} | ||
|
|
||
| # 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@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7 | ||
| 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@f2a1d5e99d037542a71f64918e516c093c6f3fc4 | ||
| with: | ||
| platforms: linux/amd64,linux/arm64 | ||
| context: . | ||
| push: true | ||
| tags: ${{ steps.meta.outputs.tags }} | ||
| labels: ${{ steps.meta.outputs.labels }} | ||
|
|
||
| # 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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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,5 @@ | ||
| 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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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,70 @@ | ||
| #!/bin/bash | ||
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| # Do not modify this file modify ${SCRIPTPATH}/etc/wrapper.conf instead! | ||
| SCRIPTPATH="$(cd "$(dirname "$0")" ; pwd -P)" | ||
| SCRIPTPATH=${SCRIPTPATH%%bin} | ||
| SCRIPTPATH=${SCRIPTPATH%%/} | ||
| GEN_SHARED_CVMFS=/tmp/cvmfs-cache | ||
| GEN_CONTAINERTYPE=singularity | ||
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| source "${SCRIPTPATH}"/etc/wrapper.conf | ||
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| mkdir -p ${GEN_SHARED_CVMFS} | ||
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| touch "$HOME/.genpipes_env" # needs to exist for the run cmd not to crash | ||
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| # If GEN_CONTAINERTYPE equals singularity | ||
| if [ "$GEN_CONTAINERTYPE" = "singularity" ]; then | ||
| if [ -z ${BIND_LIST+x} ]; then | ||
| singularity run \ | ||
| --env-file $HOME/.genpipes_env \ | ||
| --cleanenv \ | ||
| -S /var/run/cvmfs \ | ||
| -B ${GEN_SHARED_CVMFS}:/cvmfs-cache \ | ||
| --fusemount "container:cvmfs2 cvmfs-config.computecanada.ca /cvmfs/cvmfs-config.computecanada.ca" \ | ||
| --fusemount "container:cvmfs2 soft.mugqic /cvmfs/soft.mugqic" \ | ||
| --fusemount "container:cvmfs2 ref.mugqic /cvmfs/ref.mugqic" \ | ||
| ${SCRIPTPATH}/images/genpipes.sif "$@" | ||
| else | ||
| singularity run \ | ||
| --env-file $HOME/.genpipes_env \ | ||
| --cleanenv \ | ||
| -S /var/run/cvmfs \ | ||
| -B ${GEN_SHARED_CVMFS}:/cvmfs-cache \ | ||
| -B "$BIND_LIST" \ | ||
| --fusemount "container:cvmfs2 cvmfs-config.computecanada.ca /cvmfs/cvmfs-config.computecanada.ca" \ | ||
| --fusemount "container:cvmfs2 soft.mugqic /cvmfs/soft.mugqic" \ | ||
| --fusemount "container:cvmfs2 ref.mugqic /cvmfs/ref.mugqic" \ | ||
| ${SCRIPTPATH}/images/genpipes.sif "$@" | ||
| fi | ||
| elif [ "$GEN_CONTAINERTYPE" = "docker" ]; then | ||
| if [ -z ${BIND_LIST+x} ]; then | ||
| docker run \ | ||
| -it \ | ||
| --env-file $HOME/.genpipes_env \ | ||
| --rm \ | ||
| --device /dev/fuse \ | ||
| --cap-add SYS_ADMIN \ | ||
| --tmpfs /var/run/cvmfs:rw \ | ||
| -w $PWD \ | ||
| -v $PWD:$PWD \ | ||
| --mount type=bind,source=${BIND_LIST},target=${BIND_LIST} \ | ||
| --mount type=bind,source=${GEN_SHARED_CVMFS},target=/cvmfs-cache \ | ||
| c3genomics/genpipes:latest "$@" | ||
| else | ||
| docker run \ | ||
| -it \ | ||
| --env-file $HOME/.genpipes_env \ | ||
| --rm \ | ||
| --device /dev/fuse \ | ||
| --cap-add SYS_ADMIN \ | ||
| --tmpfs /var/run/cvmfs:rw \ | ||
| -w $PWD \ | ||
| -v $PWD:$PWD \ | ||
| --mount type=bind,source=${GEN_SHARED_CVMFS},target=/cvmfs-cache \ | ||
| c3genomics/genpipes:latest "$@" | ||
| fi | ||
| else | ||
| echo "Unknown GEN_CONTAINERTYPE $GEN_CONTAINERTYPE. Choose between 'singularity' or 'docker'. Exiting." | ||
| exit 1 | ||
| fi |
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1
...ity/wrapper_genpipes/etc/wrapper.conf.tpl → ...ner/wrapper_genpipes/etc/wrapper.conf.tpl
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,3 +1,4 @@ | ||
| # GEN_SHARED_CVMFS should have a sufficient amount of space to load full reference files | ||
| export GEN_SHARED_CVMFS=$HOME/cvmfs | ||
| BIND_LIST= | ||
| GEN_CONTAINERTYPE=singularity |
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