regenie/Dockerfile_mkl at master · rgcgithub/regenie · GitHub

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# Filename: Dockerfile_mkl

# make this global
ARG LIB_INSTALL
ARG LIB_INSTALL2


FROM public.ecr.aws/ubuntu/ubuntu:22.04 AS builder

ARG BOOST_IO
ARG LIB_INSTALL
ARG STATIC
ARG CMAKE_VERSION_MAJOR=3.13
ARG CMAKE_VERSION_MINOR=0
ARG HTSLIB_VERSION=1.18

WORKDIR /src

ADD http://cmake.org/files/v${CMAKE_VERSION_MAJOR}/cmake-${CMAKE_VERSION_MAJOR}.${CMAKE_VERSION_MINOR}-Linux-x86_64.sh cmake_install.sh
ADD http://code.enkre.net/bgen/tarball/release/v1.1.7 v1.1.7.tgz
ADD https://github.com/samtools/htslib/releases/download/$HTSLIB_VERSION/htslib-$HTSLIB_VERSION.tar.bz2 htslib-$HTSLIB_VERSION.tar.bz2
ADD https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB intel_key.PUB
COPY . /src/regenie

# install BGEN and HTSlib libraries
RUN apt-get update && apt-get install -y --no-install-recommends \
      gcc-9 \
      g++-9 \
      gfortran-9 \
      libz-dev \
      bzip2 \
      libbz2-dev \
      liblzma-dev \
      libcurl4-openssl-dev \
      libssl-dev \
      make \
      gnupg \
      python3 \
      zlib1g-dev \
      apt-transport-https ca-certificates \
      $LIB_INSTALL \
      && update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-9 60 --slave /usr/bin/g++ g++ /usr/bin/g++-9 \
      && update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-9 70 \
      && update-alternatives --install /usr/bin/f77 f77 /usr/bin/gfortran-9 70 \
      && update-alternatives --install /usr/bin/cc cc /usr/bin/gcc-9 70 \
      && tar -xf htslib-$HTSLIB_VERSION.tar.bz2 \
      && cd htslib-$HTSLIB_VERSION/ \
      && ./configure \
      && make \
      && make install \
      && cd .. \
      && sh cmake_install.sh --prefix=/usr/local --skip-license --exclude-subdir \
      && rm cmake_install.sh \
      && tar -xzf v1.1.7.tgz \
      && rm v1.1.7.tgz \
      && cd v1.1.7 \
      && python3 waf configure \
      && python3 waf \
      && cd .. \
      && sh -c 'cat intel_key.PUB | gpg --dearmor | tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null' \
      && sh -c 'echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | tee /etc/apt/sources.list.d/oneAPI.list' \
      && apt-get update \
      && apt-get install intel-oneapi-mkl-devel -y --no-install-recommends \
      && . /opt/intel/oneapi/setvars.sh \
      && echo "MKL_THREADING_LAYER=GNU" >> /etc/environment \
      && cd /src/regenie \
      && BGEN_PATH=/src/v1.1.7 HAS_BOOST_IOSTREAM=$BOOST_IO MKLROOT=$MKLROOT HTSLIB_PATH=/usr/local/lib/ STATIC=1 cmake . \
      && make

# no need to install Boost IO and MKL here (static linking)
FROM public.ecr.aws/ubuntu/ubuntu:22.04

RUN apt-get update && apt-get install -y --no-install-recommends \
      libgomp1 gfortran-9 \
      libz-dev libbz2-dev liblzma-dev libcurl4-openssl-dev libssl-dev \
      && rm -rf /var/lib/apt/lists/*

COPY --from=builder /src/regenie/regenie /usr/local/bin