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brentpbrentp
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fix build
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‎.github/workflows/build.yml‎

Lines changed: 141 additions & 106 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
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# copied from Daniel Cook's Seq collection
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name: Build
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on:
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on:
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push:
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branches:
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- master
@@ -13,116 +13,151 @@ on:
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jobs:
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build:
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-20.04, macos-14]
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os: [ubuntu-22.04, macos-14]
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version:
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- 1.6.18
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- 2.0.2
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- 1.6.18
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- 2.0.2
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steps:
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- uses: actions/checkout@v4
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# Caching
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- name: Cache choosenim
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id: cache-choosenim
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uses: actions/cache@v4
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with:
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path: ~/.choosenim
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key: ${{ runner.os }}-choosenim-stable
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- name: Cache nimble
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id: cache-nimble
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uses: actions/cache@v4
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with:
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path: ~/.nimble
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key: ${{ runner.os }}-nimble-stable
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- name: Cache htslib
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id: cache-htslib
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uses: actions/cache@v4
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with:
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path: $HOME/htslib
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key: ${{ runner.os }}-htslib-1.10
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# Install Dependencies
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- name: Install dependencies (Linux)
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if: runner.os == 'Linux'
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run: |
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sudo apt-get update
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sudo apt-get -qy install bwa make build-essential cmake libncurses-dev ncurses-dev libbz2-dev lzma-dev liblzma-dev \
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curl libssl-dev libtool autoconf automake libcurl4-openssl-dev zlib1g-dev
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# Setup htslib
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- name: Install htslib (linux)
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if: runner.os == 'Linux'
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run: |
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cd
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git clone -b 1.22.1 --recursive https://github.com/samtools/htslib.git
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cd htslib && autoheader && autoconf && ./configure --enable-libcurl
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sudo make -j 4 install
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sudo ldconfig
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#echo "::set-env name=LD_LIBRARY_PATH::${LD_LIBRARY_PATH}:${HOME}/htslib"
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#ls -lh $HOME/htslib/*.so
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- name: Install hstlib (macos)
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if: runner.os == 'macOS'
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run: |
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brew install htslib
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- name: Set DYLD_LIBRARY_PATH
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if: runner.os == 'macOS'
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run: |
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- uses: actions/checkout@v4
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with:
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submodules: true
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fetch-depth: 0
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# Caching
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- name: Cache choosenim
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id: cache-choosenim
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uses: actions/cache@v4
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with:
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path: ~/.choosenim
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key: ${{ runner.os }}-choosenim-stable
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- name: Cache nimble
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id: cache-nimble
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uses: actions/cache@v4
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with:
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path: ~/.nimble
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key: ${{ runner.os }}-nimble-stable
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- name: Cache htslib
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id: cache-htslib
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uses: actions/cache@v4
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with:
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path: $HOME/htslib
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key: ${{ runner.os }}-htslib-1.10
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# Install Dependencies
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- name: Install dependencies (Linux)
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if: runner.os == 'Linux'
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run: |
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sudo apt-get update
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sudo apt-get -qy install bwa make build-essential cmake libncurses-dev ncurses-dev libbz2-dev lzma-dev liblzma-dev \
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curl libssl-dev libtool autoconf automake libcurl4-openssl-dev zlib1g-dev
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# Setup htslib
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- name: Install htslib (linux)
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if: runner.os == 'Linux'
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run: |
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cd
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git clone -b 1.22.1 --recursive https://github.com/samtools/htslib.git
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cd htslib && autoheader && autoconf && autoreconf -i && ./configure --enable-libcurl
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sudo make -j 4 install
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sudo ldconfig
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#echo "::set-env name=LD_LIBRARY_PATH::${LD_LIBRARY_PATH}:${HOME}/htslib"
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#ls -lh $HOME/htslib/*.so
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- name: Install hstlib (macos)
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if: runner.os == 'macOS'
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run: |
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brew install htslib
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- name: Set DYLD_LIBRARY_PATH
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if: runner.os == 'macOS'
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run: |
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echo "DYLD_LIBRARY_PATH=$(brew --prefix htslib)/lib" >> $GITHUB_ENV
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- name: Install d4
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run: |
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#export HTSLIB=system
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git clone https://github.com/38/d4-format
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echo 'location' >> ~/.curlrc # https://github.com/38/d4-format/pull/77#issuecomment-2044438359
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cd d4-format
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cargo build --release --all-features --package=d4binding
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sudo cp target/release/libd4binding.* /usr/local/lib
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sudo cp d4binding/include/d4.h /usr/local/include/
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sudo ldconfig || true
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- uses: iffy/install-nim@v5
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with:
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version: ${{ matrix.version }}
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- name: Rust Toolchain
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uses: dtolnay/rust-toolchain@nightly
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with:
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toolchain: stable
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# Build and Test
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- name: Build test executable
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run: nimble build -Y mosdepth.nimble
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- name: "Copy binary"
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run: chmod +x mosdepth && mkdir bin && cp mosdepth bin/mosdepth_debug_${{ matrix.os }}
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- name: "Build and Copy release binary"
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run: nim c --mm:refc -d:danger -d:release -o:bin/mosdepth_${{ matrix.os }} mosdepth
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- name: Functional Tests
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env:
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TERM: "xterm"
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run: |
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bash ./functional-tests.sh
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- name: Unit Tests
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run: |
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nim c -r tests/all.nim
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- name: Upload Artifact
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if: success()
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uses: actions/upload-artifact@v4
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with:
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name: mosdepth_${{ matrix.os }}_nim${{ matrix.version }}_executable
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path: bin/
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echo "DYLD_INCLUDE_PATH=$(brew --prefix htslib)/include" >> $GITHUB_ENV
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echo "LIBRARY_PATH=$(brew --prefix htslib)/lib" >> $GITHUB_ENV
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echo "CPATH=$(brew --prefix htslib)/include" >> $GITHUB_ENV
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- name: Set DYLD_LIBRARY_PATH (Linux)
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if: runner.os == 'Linux'
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run: |
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echo "DYLD_LIBRARY_PATH=/usr/local/lib" >> $GITHUB_ENV
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echo "DYLD_INCLUDE_PATH=/usr/local/include" >> $GITHUB_ENV
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- name: Make libhts discoverable for tests
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run: |
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# Detect htslib location via Homebrew or fallback to $HOME/htslib
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HTS_LIB_DIR=""
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if command -v brew >/dev/null 2>&1; then
97+
BREW_PREFIX="$(brew --prefix htslib 2>/dev/null || true)"
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if [ -n "$BREW_PREFIX" ] && [ -d "$BREW_PREFIX/lib" ]; then
99+
HTS_LIB_DIR="$BREW_PREFIX/lib"
100+
fi
101+
fi
102+
if [ -z "$HTS_LIB_DIR" ] && [ -d "$HOME/htslib" ]; then
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HTS_LIB_DIR="$HOME/htslib"
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fi
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if [ -z "$HTS_LIB_DIR" ]; then
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echo "ERROR: libhts not found via Homebrew or at \$HOME/htslib" >&2
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exit 1
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fi
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echo "Using htslib dir: $HTS_LIB_DIR"
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if [ "${RUNNER_OS:-}" = "macOS" ]; then
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#echo "DYLD_LIBRARY_PATH=$HTS_LIB_DIR:${DYLD_LIBRARY_PATH:-}" >> "$GITHUB_ENV"
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echo "DYLD_LIBRARY_PATH=$HTS_LIB_DIR" >> "$GITHUB_ENV"
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else
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#echo "LD_LIBRARY_PATH=$HTS_LIB_DIR:${LD_LIBRARY_PATH:-}" >> "$GITHUB_ENV"
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echo "LD_LIBRARY_PATH=$HTS_LIB_DIR" >> "$GITHUB_ENV"
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fi
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- name: Install d4
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run: |
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#export HTSLIB=system
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git clone https://github.com/38/d4-format
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echo 'location' >> ~/.curlrc # https://github.com/38/d4-format/pull/77#issuecomment-2044438359
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cd d4-format
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cargo build --release --all-features --package=d4binding
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sudo cp target/release/libd4binding.* $DYLD_LIBRARY_PATH
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sudo cp d4binding/include/d4.h $DYLD_INCLUDE_PATH
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sudo ldconfig || true
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- uses: iffy/install-nim@v5
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with:
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version: ${{ matrix.version }}
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- name: Rust Toolchain
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uses: dtolnay/rust-toolchain@nightly
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with:
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toolchain: stable
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# Build and Test
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- name: Build test executable
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run: nimble build -Y mosdepth.nimble
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- name: "Copy binary"
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run: chmod +x mosdepth && mkdir bin && cp mosdepth bin/mosdepth_debug_${{ matrix.os }}
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- name: "Build and Copy release binary"
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run: nim c --mm:refc -d:danger -d:release -o:bin/mosdepth_${{ matrix.os }} mosdepth
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- name: Functional Tests
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env:
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TERM: "xterm"
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run: |
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bash ./functional-tests.sh
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- name: Unit Tests
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run: |
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nim c -r tests/all.nim
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- name: Upload Artifact
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if: success()
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uses: actions/upload-artifact@v4
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with:
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name: mosdepth_${{ matrix.os }}_nim${{ matrix.version }}_executable
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path: bin/

‎mosdepth.nimble‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@ license = "MIT"
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# Dependencies
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10-
requires "hts >= 0.3.27", "docopt == 0.7.1", "nim >= 1.0.0", "https://github.com/brentp/d4-nim >= 0.0.5"
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requires "hts >= 0.3.29", "docopt == 0.7.1", "nim >= 1.0.0", "https://github.com/brentp/d4-nim >= 0.0.5"
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bin = @["mosdepth"]
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skipDirs = @["tests"]

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