EVA-3586 - Allow colon in chromosome names #44
Workflow file for this run
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| name: Build | |
| on: | |
| pull_request: | |
| branches: | |
| - master | |
| push: | |
| branches: | |
| - master | |
| tags: | |
| - '*' | |
| jobs: | |
| ### Linux build | |
| linux_build: | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| matrix: | |
| config: | |
| - {cc: "gcc", cxx: "g++"} | |
| - {cc: "clang-10", cxx: "clang++-10"} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install libsqlite3-0 libsqlite3-dev cmake wget build-essential | |
| ./install_dependencies.sh linux | |
| - name: Compile and test | |
| run: | | |
| mkdir build && cd build && cmake -G "Unix Makefiles" -DCMAKE_CXX_COMPILER=${{ matrix.config.cxx }} -DCMAKE_C_COMPILER=${{ matrix.config.cc }} .. | |
| make -j2 | |
| cd .. && ./build/bin/test_validation_suite | |
| - name: Rename release files | |
| if: ${{ matrix.config.cc == 'gcc' }} | |
| run: | | |
| mv build/bin/vcf_validator vcf_validator_linux | |
| mv build/bin/vcf_debugulator vcf_debugulator_linux | |
| mv build/bin/vcf_assembly_checker vcf_assembly_checker_linux | |
| - name: Upload vcf-validator | |
| uses: actions/upload-artifact@v3 | |
| if: ${{ matrix.config.cc == 'gcc' }} | |
| with: | |
| name: vcf_validator_linux | |
| path: vcf_validator_linux | |
| - name: Upload vcf-debugulator | |
| uses: actions/upload-artifact@v3 | |
| if: ${{ matrix.config.cc == 'gcc' }} | |
| with: | |
| name: vcf_debugulator_linux | |
| path: vcf_debugulator_linux | |
| - name: Upload vcf-assembly-checker | |
| uses: actions/upload-artifact@v3 | |
| if: ${{ matrix.config.cc == 'gcc' }} | |
| with: | |
| name: vcf_assembly_checker_linux | |
| path: vcf_assembly_checker_linux | |
| ### Mac OS build | |
| macos_build: | |
| runs-on: macos-12 | |
| strategy: | |
| matrix: | |
| config: | |
| - {cc: "gcc", cxx: "g++"} | |
| - {cc: "clang", cxx: "clang++"} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install dependencies | |
| run: | | |
| #brew update | |
| HOMEBREW_NO_AUTO_UPDATE=1 brew install boost sqlite3 automake | |
| ./install_dependencies.sh osx | |
| - name: Compile and test | |
| run: | | |
| mkdir build && cd build && cmake -G "Unix Makefiles" -DCMAKE_CXX_COMPILER=${{ matrix.config.cxx }} -DCMAKE_C_COMPILER=${{ matrix.config.cc }} .. | |
| export LIBRARY_PATH=${LIBRARY_PATH}:/usr/local/opt/icu4c/lib:/usr/local/lib | |
| make -j2 | |
| cd .. && ./build/bin/test_validation_suite | |
| - name: Rename release files | |
| if: ${{ matrix.config.cc == 'clang' }} | |
| run: | | |
| mv build/bin/vcf_validator vcf_validator_macos | |
| mv build/bin/vcf_debugulator vcf_debugulator_macos | |
| mv build/bin/vcf_assembly_checker vcf_assembly_checker_macos | |
| - name: Upload vcf-validator | |
| uses: actions/upload-artifact@v3 | |
| if: ${{ matrix.config.cc == 'clang' }} | |
| with: | |
| name: vcf_validator_macos | |
| path: vcf_validator_macos | |
| - name: Upload vcf-debugulator | |
| uses: actions/upload-artifact@v3 | |
| if: ${{ matrix.config.cc == 'clang' }} | |
| with: | |
| name: vcf_debugulator_macos | |
| path: vcf_debugulator_macos | |
| - name: Upload vcf-assembly-checker | |
| uses: actions/upload-artifact@v3 | |
| if: ${{ matrix.config.cc == 'clang' }} | |
| with: | |
| name: vcf_assembly_checker_macos | |
| path: vcf_assembly_checker_macos | |
| ### Release job (tags only) | |
| create_release: | |
| if: startsWith(github.ref, 'refs/tags/') | |
| needs: [ linux_build, macos_build ] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Download artifacts | |
| uses: actions/download-artifact@v3 | |
| with: | |
| path: bin | |
| - name: Draft release | |
| uses: softprops/action-gh-release@v1 | |
| with: | |
| draft: true | |
| files: ${{ github.workspace }}/bin/*/* | |
| fail_on_unmatched_files: true |