Dockerfile tests and cleanup imputation/PRS #25
Workflow file for this run
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| name: Dockerfile tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| paths: | |
| - '**/Dockerfile' | |
| schedule: | |
| - cron: '23 2 * * 0' | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| define_changed_dockerfile_matrix: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.changed-dockerfiles.outputs.all_changed_files }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - | |
| name: Get Changed Dockerfiles | |
| id: changed-dockerfiles | |
| uses: tj-actions/changed-files@v44 | |
| with: | |
| matrix: true | |
| files: '**/Dockerfile' | |
| files_ignore: '**/GlimpseImputationPipeline/glimpse_docker/Dockerfile' | |
| - name: List dockerfiles | |
| run: echo '${{ steps.changed-dockerfiles.outputs.all_changed_files}}' | |
| define_all_dockerfile_matrix: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.all-dockerfiles.outputs.files}} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - | |
| name: Get all Dockerfiles | |
| id: all-dockerfiles | |
| run: | | |
| { | |
| echo 'files<<EOF' | |
| find . -name "Dockerfile" ! -path "*/GlimpseImputationPipeline/glimpse_docker/*" | jq -R . | jq -s . | |
| echo EOF | |
| } >> "$GITHUB_OUTPUT" | |
| - name: List dockerfiles | |
| run: echo '${{ steps.all-dockerfiles.outputs.files}}' | |
| test_builds: | |
| runs-on: ubuntu-latest | |
| needs: [define_changed_dockerfile_matrix, define_all_dockerfile_matrix] | |
| strategy: | |
| matrix: | |
| #change github.ref check to refs/heads/main | |
| dockerfile: ${{ github.ref != 'refs/pull/202/merge' && fromJSON(needs.define_changed_dockerfile_matrix.outputs.matrix) || fromJSON(needs.define_all_dockerfile_matrix.outputs.matrix) }} | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - | |
| name: Get context | |
| id: get-context | |
| run: | | |
| echo "context=$(dirname ${{ matrix.dockerfile }})" >> $GITHUB_OUTPUT | |
| - | |
| name: Setup Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - | |
| name: Build | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: ${{ steps.get-context.outputs.context }} | |
| file: ${{ matrix.dockerfile }} | |
| cache-from: type=gha | |
| cache-to: type=gha, mode=max | |
| test_glimpse_docker: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - | |
| name: Check if Dockerfile has changed | |
| id: check-if-changed | |
| #change github.ref check to refs/heads/main | |
| if: ${{ github.ref != 'refs/pull/202/merge' }} | |
| uses: tj-actions/changed-files@v44 | |
| with: | |
| files: '**/GlimpseImputationPipeline/glimpse_docker/Dockerfile' | |
| - | |
| name: Build main GLIMPSE Docker | |
| #change github.ref check to refs/heads/main | |
| if: ${{ github.ref == 'refs/pull/202/merge' || steps.check-if-changed.outputs.all_changed_files_count > 0 }} | |
| run: | | |
| cd GlimpseImputationPipeline/glimpse_docker | |
| ./build_base_and_extension_docker.sh -r https://github.com/odelaneau/GLIMPSE.git -t test -b master -y | |
| - | |
| name: Build Extract Num Sites Docker | |
| #change github.ref check to refs/heads/main | |
| if: ${{ github.ref == 'refs/pull/202/merge' || steps.check-if-changed.outputs.all_changed_files_count > 0 }} | |
| run: | | |
| cd GlimpseImputationPipeline/glimpse_docker | |
| ./build_extract_num_sites_from_reference_chunk_docker.sh -y -r https://github.com/michaelgatzen/GLIMPSE.git -t test -b master | |