Deploy Apptainer #5
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| name: Deploy Apptainer | |
| on: | |
| workflow_run: | |
| workflows: ["release-please"] | |
| types: | |
| - completed | |
| workflow_dispatch: | |
| jobs: | |
| build_and_push: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| packages: write | |
| if: ${{ github.event_name == 'workflow_dispatch' || github.event.workflow_run.conclusion == 'success' }} | |
| steps: | |
| - name: checkout repo | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: add apptainer source | |
| shell: bash | |
| run: | | |
| sudo add-apt-repository -y ppa:apptainer/ppa | |
| sudo apt-get update | |
| - name: create dockerfile | |
| uses: snakemake/snakemake-github-action@v2 | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| install-apptainer: true | |
| args: "--cores 1" | |
| task: containerize | |
| - name: create apptainer recipe | |
| shell: bash | |
| run: | | |
| pip install spython | |
| sed -i "2i RUN apt-get update && apt-get install -y curl" Dockerfile | |
| spython recipe Dockerfile > apptainer.def | |
| sed -i 's/\/environment.yaml\/environment.yaml$/\/environment.yaml/' apptainer.def | |
| - name: create apptainer image | |
| shell: bash | |
| run: | | |
| sudo apt-get install -y uidmap | |
| apptainer build --fakeroot apptainer.sif apptainer.def | |
| - name: authenticate to GHCR | |
| run: | | |
| echo ${{ secrets.GITHUB_TOKEN }} | apptainer registry login -u ${{ github.actor }} --password-stdin oras://ghcr.io | |
| - name: push apptainer to GHCR | |
| run: | | |
| REPO=$(echo "${{ github.repository }}" | tr '[:upper:]' '[:lower:]') | |
| echo "Pushing apptainer to: oras://ghcr.io/${REPO}:latest" | |
| apptainer push apptainer.sif "oras://ghcr.io/${REPO}:latest" |