Merge pull request #62 from marbl/htslib-optional #20
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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: Align yeast genomes | |
| 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 '#' | |
| --threads $(nproc --all) | |
| -o scerevisiae8.paf; | |
| - name: Test yeast coverage | |
| run: scripts/test.sh data/scerevisiae8.fa.gz.fai scerevisiae8.paf 0.92 | |