Merge pull request #676 from KimBioInfoStudio/fix/stale-overlap-merge… #155
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| name: fastp ci | |
| on: | |
| push: | |
| branches: [master] | |
| pull_request: | |
| branches: [master] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| build: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v4 | |
| - name: install dependencies (Ubuntu) | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y build-essential nasm | |
| - name: build ISA-L static (Ubuntu) | |
| if: runner.os == 'Linux' | |
| run: | | |
| git clone --depth=1 --branch v2.31.1 https://github.com/intel/isa-l.git /tmp/isa-l | |
| cd /tmp/isa-l | |
| ./autogen.sh | |
| ./configure --prefix=/usr/local --enable-static --disable-shared | |
| make -j$(nproc) | |
| sudo make install | |
| - name: build libdeflate static (Ubuntu) | |
| if: runner.os == 'Linux' | |
| run: | | |
| git clone --depth=1 --branch v1.23 https://github.com/ebiggers/libdeflate.git /tmp/libdeflate | |
| cd /tmp/libdeflate | |
| cmake -B _build -DCMAKE_BUILD_TYPE=Release \ | |
| -DLIBDEFLATE_BUILD_STATIC_LIB=ON -DLIBDEFLATE_BUILD_SHARED_LIB=OFF \ | |
| -DLIBDEFLATE_BUILD_GZIP=OFF -DCMAKE_INSTALL_PREFIX=/usr/local | |
| cmake --build _build -j$(nproc) | |
| sudo cmake --install _build | |
| - name: install dependencies (macOS) | |
| if: runner.os == 'macOS' | |
| run: brew install libdeflate isa-l | |
| - name: build Highway | |
| run: | | |
| git clone --depth=1 --branch 1.3.0 https://github.com/google/highway.git /tmp/highway | |
| cd /tmp/highway | |
| cmake -B _build -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=OFF \ | |
| -DHWY_ENABLE_TESTS=OFF -DHWY_ENABLE_EXAMPLES=OFF \ | |
| -DCMAKE_INSTALL_PREFIX=/usr/local | |
| cmake --build _build -j$(nproc 2>/dev/null || sysctl -n hw.ncpu) | |
| sudo cmake --install _build | |
| - name: build fastp | |
| run: make -j$(nproc 2>/dev/null || sysctl -n hw.ncpu) | |
| - name: smoke test | |
| run: | | |
| ./fastp --version | |
| ./fastp -i testdata/R1.fq -o /dev/null |