make-binary-linux.yml

name: Make binary (Linux)

on:
  workflow_dispatch:

env:
  CONTAINER: andrewdavidsmith/transferase-build

jobs:
  make-binary-linux:
    runs-on: ubuntu-latest
    steps:
      - name: Start docker container
        # Pull the container, run it in detached mode, mount the workspace
        run: |
          docker pull $CONTAINER
          docker run --name build-container \
          -d -v ${{ github.workspace }}:/workspace $CONTAINER tail -f /dev/null
      - uses: actions/checkout@v6
        with:
          submodules: recursive
      - name: Get version number
        id: get-vn
        run: |
          awk '/^  VERSION [0-9.]+$/ {print "vn="$NF}' CMakeLists.txt >> "$GITHUB_OUTPUT"
          git rev-parse --short "$GITHUB_SHA" | awk '{print "hash="$0}' >> "$GITHUB_OUTPUT"
        env:
          GH_TOKEN: ${{ github.token }}
      - name: Configure and build
        env:
          SCRIPT: |
            export DEBIAN_FRONTEND=noninteractive && \
            apt-get update && apt-get install --no-install-recommends -y automake wget && \
            wget -nv https://www.nasm.us/pub/nasm/releasebuilds/3.01rc9/nasm-3.01rc9.tar.gz && \
            tar -xf nasm-3.01rc9.tar.gz && \
            cd nasm-3.01rc9 && \
            ./configure --prefix=/usr/local && \
            make -j4 && \
            make install && \
            cd .. && \
            git clone https://github.com/intel/isa-l.git && \
            cd isa-l && \
            cmake -B build \
                -DISAL_BUILD_TESTS=off \
                -DISAL_BUILD_PERF_TESTS=off \
                -DISAL_BUILD_FUZZ_TESTS=off \
                -DISAL_BUILD_ISAL_SHIM=off \
                -DBUILD_SHARED_LIBS=off \
                -DCMAKE_BUILD_TYPE=Release && \
            cmake --build build -j4 && \
            cmake --install build --prefix=/usr/local && \
            cd ../ && \
            git clone https://github.com/ebiggers/libdeflate.git && \
            cd libdeflate && \
            cmake -B build \
                -DLIBDEFLATE_BUILD_GZIP=off \
                -DLIBDEFLATE_BUILD_TESTS=off \
                -DLIBDEFLATE_BUILD_SHARED_LIB=off \
                -DCMAKE_VERBOSE_MAKEFILE=on \
                -DCMAKE_BUILD_TYPE=Release && \
            cmake --build build -j4 && \
            cmake --install build --prefix=/usr/local && \
            cd .. && \
            git clone --recursive https://github.com/samtools/htslib.git && \
            cd htslib && \
            autoreconf -i && \
            mkdir build && cd build && \
            ../configure \
                --disable-bz2 \
                --disable-libcurl \
                --disable-lzma \
                --disable-ref-cache \
                --with-libdeflate && \
            make -j4 CFLAGS="-Wall -O2 -fvisibility=hidden" libhts.a && \
            cp libhts.a /usr/local/lib/ && \
            cp -r ../htslib /usr/local/include/ && \
            cd /workspace && \
            cmake -B build \
                -DPACKAGE=on \
                -DCMAKE_VERBOSE_MAKEFILE=on \
                -DUSE_ISAL=on \
                -DCMAKE_BUILD_TYPE=Release && \
            cmake --build build -j4 && \
            cp build/falco falco-${{ steps.get-vn.outputs.vn }}-${{ steps.get-vn.outputs.hash }}-Linux
        run: |
          docker exec build-container bash -c "$SCRIPT"
      - name: Upload the binary
        uses: actions/upload-artifact@v7
        with:
          name: falco-${{ steps.get-vn.outputs.vn }}-${{ steps.get-vn.outputs.hash }}-Linux
          path: falco-${{ steps.get-vn.outputs.vn }}-${{ steps.get-vn.outputs.hash }}-Linux