dnmtools_release_linux.yml

name: DNMTools release (Linux)

on:
  workflow_dispatch:

env:
  CONTAINER: andrewdavidsmith/builder

jobs:
  linux-releases:
    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@v4
        with:
          submodules: recursive
      - name: Get version number
        id: get-vn
        run: |
          awk '/AC_INIT/ {print "vn="$2}' configure.ac | sed "s/\[//; s/\]//; s/,//" >> "$GITHUB_OUTPUT"
        env:
          GH_TOKEN: ${{ github.token }}
      - name: Configure and build
        env:
          SCRIPT: |
            export DEBIAN_FRONTEND=noninteractive && \
            apt-get update && apt-get install --no-install-recommends -y libgsl-dev && \
            find /usr -name libz.so -exec rm {} \; && \
            find /usr -name libgsl\*.so -exec rm {} \; && \
            git clone https://github.com/ebiggers/libdeflate.git && \
            cd libdeflate && \
            cmake -B build \
                -DLIBDEFLATE_BUILD_GZIP=off \
                -DLIBDEFLATE_BUILD_TESTS=off \
                -DLIBDEFLATE_BUILD_SHARED_LIB=off \
                -DCMAKE_VERBOSE_MAKEFILE=on \
                -DCMAKE_BUILD_TYPE=Release && \
            cmake --build build -j4 && \
            cmake --install build --prefix=/usr/local && \
            cd .. && \
            git clone --recursive https://github.com/samtools/htslib.git && \
            cd htslib && \
            autoreconf -i && \
            mkdir build && cd build && \
            ../configure \
                --disable-bz2 \
                --disable-libcurl \
                --disable-lzma \
                --disable-ref-cache \
                --with-libdeflate && \
            make -j4 CFLAGS="-Wall -O2 -fvisibility=hidden" libhts.a && \
            cp libhts.a /usr/local/lib/ && \
            cp -r ../htslib /usr/local/include/ && \
            cd /workspace && \
            autoreconf -i && \
            mkdir build && cd build && \
            ../configure --with-libdeflate --with-htsmods && \
            ../data/make_full_license_info_header.sh ../data/LICENSE > license.h && \
            echo "#define INCLUDE_FULL_LICENSE_INFO 1" >> config.h && \
            make -j4 LDFLAGS="-static-libgcc -static-libstdc++ -s" && \
            tar -cf dnmtools-${{ steps.get-vn.outputs.vn }}-Linux.tar.gz dnmtools
        run: |
          docker exec build-container bash -c "$SCRIPT"
      - name: Upload the binary
        uses: actions/upload-artifact@v4
        with:
          name: dnmtools-${{ steps.get-vn.outputs.vn }}-Linux.tar.gz
          path: build/dnmtools-${{ steps.get-vn.outputs.vn }}-Linux.tar.gz