Workflow file for this run
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| name: Build and test mapping coverage | ||
| on: | ||
| push: | ||
| branches: [ master ] | ||
| paths-ignore: | ||
| - '**/*.md' | ||
| pull_request: | ||
| branches: [ master ] | ||
| paths-ignore: | ||
| - '**/*.md' | ||
| env: | ||
| # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.) | ||
| BUILD_TYPE: DEBUG | ||
| jobs: | ||
| linux: | ||
| # 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 }} | ||
| strategy: | ||
| matrix: | ||
| os: [ubuntu-20.04] | ||
| compiler: | ||
| - { compiler: GNU, CC: gcc-11, CXX: g++-11 } | ||
| steps: | ||
| - name: Cancel Workflow Action | ||
| uses: styfle/[email protected] | ||
| - name: Checkout | ||
| uses: actions/checkout@v2 | ||
| with: | ||
| submodules: 'true' | ||
| - name: Setup apt | ||
| run: | ||
| - sudo apt install build-essential manpages-dev software-properties-common | ||
| - sudo add-apt-repository ppa:ubuntu-toolchain-r/test | ||
| - sudo apt update && sudo apt install | ||
| - name: Install Requirements | ||
| run: sudo apt install -y | ||
| ${{ matrix.compiler.CC }} | ||
| ${{ matrix.compiler.CXX }} | ||
| libhts-dev | ||
| libjemalloc-dev | ||
| libgsl-dev | ||
| zlib1g-dev | ||
| libhts-dev | ||
| samtools | ||
| bedtools | ||
| - name: Build | ||
| env: | ||
| CC: ${{ matrix.compiler.CC }} | ||
| CXX: ${{ matrix.compiler.CXX }} | ||
| # Build your program with the given configuration | ||
| run: cmake -H. -Bbuild -DCMAKE_BUILD_TYPE=${BUILD_TYPE} && cmake --build build -- | ||
| - name: Basic version test | ||
| env: | ||
| CC: ${{ matrix.compiler.CC }} | ||
| CXX: ${{ matrix.compiler.CXX }} | ||
| run: build/bin/mashmap -v | ||
| - name: Test coverage | ||
| env: | ||
| CC: ${{ matrix.compiler.CC }} | ||
| CXX: ${{ matrix.compiler.CXX }} | ||
| run: | | ||
| ASAN_OPTIONS=detect_leaks=1:symbolize=1 LSAN_OPTIONS=verbosity=0:log_threads=1 build/bin/mashmap \ | ||
| -r data/scerevisiae8.fa.gz | ||
| -q data/scerevisiae8.fa.gz | ||
| --pi 95 -n 1 -Y '#' | ||
| -o scerevisiae8.paf; | ||
| scripts/test.sh data/scerevisiae8.fa.gz.fai scerevisiae8.paf 0.92 | ||
