Freesurfer TRE image #95
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| --- | |
| name: main | |
| on: | |
| push: | |
| pull_request: | |
| workflow_dispatch: | |
| # schedule: | |
| # - cron: "0 6 * * *" | |
| defaults: | |
| run: | |
| shell: bash | |
| jobs: | |
| containers: | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| matrix: | |
| package: ["FSL", "Freesurfer"] | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 2 | |
| - name: skip if unchanged | |
| run: | | |
| set -euxo pipefail | |
| SKIP=0 | |
| if ! git diff --name-only HEAD^ | grep "software/${{ matrix.package }}" | grep -v README > /dev/null | |
| then | |
| SKIP=1 | |
| fi | |
| echo "SKIP=$SKIP" >> "$GITHUB_ENV" | |
| - name: Run jlumbroso/free-disk-space@main | |
| if: env.SKIP == '0' | |
| uses: jlumbroso/free-disk-space@main | |
| with: | |
| tool-cache: true | |
| docker-images: false | |
| - name: build image | |
| if: env.SKIP == '0' | |
| run: | | |
| set -euxo pipefail | |
| package="${{ matrix.package }}" | |
| cd "software/$package" | |
| img="ghcr.io/smi/${package,,}" | |
| tag="$(grep _VERSION= Dockerfile | cut -d'"' -f2)" | |
| docker build . --tag "$img:$tag" | |
| docker tag "$img:$tag" "$img:latest" | |
| echo "img=$img" >> "$GITHUB_ENV" | |
| echo "tag=$tag" >> "$GITHUB_ENV" | |
| - name: free disk space | |
| if: env.SKIP == '0' | |
| run: | | |
| set -euxo pipefail | |
| df -h | |
| docker builder prune -a -f | |
| docker rmi -f $(docker image ls -a | grep -E "(node|debian|moby|ubuntu|alpine)" | awk 'NR>1 {print $3}') | |
| df -h | |
| # debug | |
| docker image ls -a --digests --no-trunc | |
| - name: run trivy | |
| if: env.SKIP == '0' | |
| uses: aquasecurity/trivy-action@master | |
| with: | |
| image-ref: "${{ env.img }}:${{ env.tag }}" | |
| format: 'github' | |
| output: 'dependency-results.sbom.json' | |
| github-pat: "${{ secrets.GITHUB_TOKEN }}" | |
| severity: 'MEDIUM,CRITICAL,HIGH' | |
| scanners: "vuln" | |
| - name: upload trivy report | |
| if: env.SKIP == '0' && !cancelled() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: 'trivy-sbom-report-${{ matrix.package }}' | |
| path: 'dependency-results.sbom.json' | |
| - name: push image | |
| if: env.SKIP == '0' && github.ref == 'refs/heads/main' | |
| run: | | |
| set -euxo pipefail | |
| echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u $ --password-stdin | |
| docker push "$img:$tag" | |
| docker push "$img:latest" |