Allow using multiple threads to (de)compress hts files #62
Workflow file for this run
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| name: Integration Test | |
| 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: | |
| create-env: | |
| name: ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Create environment with mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| mamba-version: "*" | |
| channels: conda-forge,bioconda,defaults | |
| - 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/1.18/htslib-1.18.tar.bz2 && tar -vxjf htslib-1.18.tar.bz2 && cd htslib-1.18 && ./configure && make && sudo make install && cd ../ && rm htslib-1.18.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: Install packages | |
| run: | | |
| mamba install -c bioconda pysam picard | |
| - name: Run leviosam-test | |
| run: | | |
| cd testdata | |
| python ../leviosam-test.py ../build/leviosam2 |