Full fragment coverage mode for proper pairs #113
Workflow file for this run
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| # copied from Daniel Cook's Seq collection | |
| name: Build | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-20.04, macos-13] | |
| version: | |
| - 1.6.18 | |
| - 2.0.2 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| # Caching | |
| - name: Cache choosenim | |
| id: cache-choosenim | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.choosenim | |
| key: ${{ runner.os }}-choosenim-stable | |
| - name: Cache nimble | |
| id: cache-nimble | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.nimble | |
| key: ${{ runner.os }}-nimble-stable | |
| - name: Cache htslib | |
| id: cache-htslib | |
| uses: actions/cache@v4 | |
| with: | |
| path: $HOME/htslib | |
| key: ${{ runner.os }}-htslib-1.10 | |
| # Install Dependencies | |
| - name: Install dependencies (Linux) | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get -qy install bwa make build-essential cmake libncurses-dev ncurses-dev libbz2-dev lzma-dev liblzma-dev \ | |
| curl libssl-dev libtool autoconf automake libcurl4-openssl-dev zlib1g-dev | |
| # Setup htslib | |
| - name: Install htslib (linux) | |
| if: runner.os == 'Linux' | |
| run: | | |
| cd | |
| git clone -b 1.18 --recursive https://github.com/samtools/htslib.git | |
| cd htslib && autoheader && autoconf && ./configure --enable-libcurl | |
| sudo make -j 4 install | |
| sudo ldconfig | |
| #echo "::set-env name=LD_LIBRARY_PATH::${LD_LIBRARY_PATH}:${HOME}/htslib" | |
| #ls -lh $HOME/htslib/*.so | |
| - name: Install hstlib (macos) | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install htslib | |
| - name: Set DYLD_LIBRARY_PATH | |
| if: runner.os == 'macOS' | |
| run: | | |
| echo "DYLD_LIBRARY_PATH=$(brew --prefix htslib)/lib" >> $GITHUB_ENV | |
| - name: Install d4 | |
| run: | | |
| #export HTSLIB=system | |
| git clone https://github.com/38/d4-format | |
| echo 'location' >> ~/.curlrc # https://github.com/38/d4-format/pull/77#issuecomment-2044438359 | |
| cd d4-format | |
| cargo build --release --all-features --package=d4binding | |
| sudo cp target/release/libd4binding.* /usr/local/lib | |
| sudo cp d4binding/include/d4.h /usr/local/include/ | |
| sudo ldconfig || true | |
| - uses: iffy/install-nim@v5 | |
| with: | |
| version: ${{ matrix.version }} | |
| - name: Rust Toolchain | |
| uses: dtolnay/rust-toolchain@nightly | |
| with: | |
| toolchain: stable | |
| # Build and Test | |
| - name: Build test executable | |
| run: nimble build -Y mosdepth.nimble | |
| - name: "Copy binary" | |
| run: chmod +x mosdepth && mkdir bin && cp mosdepth bin/mosdepth_debug_${{ matrix.os }} | |
| - name: "Build and Copy release binary" | |
| run: nim c --mm:refc -d:danger -d:release -o:bin/mosdepth_${{ matrix.os }} mosdepth | |
| - name: Functional Tests | |
| env: | |
| TERM: "xterm" | |
| run: | | |
| bash ./functional-tests.sh | |
| - name: Unit Tests | |
| run: | | |
| nim c -r tests/all.nim | |
| - name: Upload Artifact | |
| if: success() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: mosdepth_${{ matrix.os }}_nim${{ matrix.version }}_executable | |
| path: bin/ |