Allow using multiple threads to (de)compress hts files #41
Workflow file for this run
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| name: Build and ctest | |
| on: | |
| push: | |
| branches: [ main ] | |
| paths: | |
| - '.github/**' | |
| - 'src/**' | |
| - 'leviosam-test.py' | |
| - 'CMakeLists.txt' | |
| - 'CMakeLists.txt.in' | |
| - 'testdata/**' | |
| pull_request: | |
| branches: | |
| - 'main' | |
| paths: | |
| - '.github/**' | |
| - 'src/**' | |
| - 'leviosam-test.py' | |
| - 'CMakeLists.txt' | |
| - 'CMakeLists.txt.in' | |
| - 'testdata/**' | |
| env: | |
| # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.) | |
| BUILD_TYPE: Release | |
| jobs: | |
| htslib_matrix: | |
| strategy: | |
| matrix: | |
| version: [1.12, 1.13, 1.14, 1.15, 1.16, 1.17, 1.18] | |
| os: [ubuntu-22.04, ubuntu-20.04, ubuntu-latest] | |
| # The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac. | |
| # You can convert this to a matrix build if you need cross-platform coverage. | |
| # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up SDSL | |
| run: sudo apt-get -y install libsdsl-dev | |
| - name: Set up htslib | |
| run: wget https://github.com/samtools/htslib/releases/download/${{ matrix.version }}/htslib-${{ matrix.version }}.tar.bz2 && tar -vxjf htslib-${{ matrix.version }}.tar.bz2 && cd htslib-${{ matrix.version }} && ./configure && make && sudo make install && cd ../ && rm htslib-${{ matrix.version }}.tar.bz2 | |
| - name: Configure CMake | |
| # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make. | |
| # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type | |
| run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} | |
| - name: Build | |
| # Build your program with the given configuration | |
| run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}} | |
| - name: Test | |
| working-directory: ${{github.workspace}}/build | |
| # Execute tests defined by the CMake configuration. | |
| # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail | |
| run: ctest -C ${{env.BUILD_TYPE}} |