Dockerfile.centos7

#
# Copyright (c) 2019, NVIDIA CORPORATION.  All rights reserved.
#
# NVIDIA CORPORATION and its licensors retain all intellectual property
# and proprietary rights in and to this software, related documentation
# and any modifications thereto.  Any use, reproduction, disclosure or
# distribution of this software and related documentation without an express
# license agreement from NVIDIA CORPORATION is strictly prohibited.
#

ARG FROM_IMAGE=gpuci/miniconda-cuda
ARG CUDA_VER=10.0
ARG LINUX_VERSION=centos7
ARG IMAGE_TYPE=devel
FROM ${FROM_IMAGE}:${CUDA_VER}-${IMAGE_TYPE}-${LINUX_VERSION}

# Capture arguments used for FROM
ARG CUDA_VER

ARG CC_VERSION=7
ARG PYTHON_VERSION=3.6
ARG CENTOS7_GCC7_URL=https://gpuci.s3.us-east-2.amazonaws.com/builds/gcc7.tgz

# Update environment for gcc/g++ builds
ENV GCC7_DIR=/usr/local/gcc7
ENV CC=${GCC7_DIR}/bin/gcc
ENV CXX=${GCC7_DIR}/bin/g++
ENV CUDAHOSTCXX=${GCC7_DIR}/bin/g++
ENV CUDA_HOME=/usr/local/cuda
ENV LD_LIBRARY_PATH=${GCC7_DIR}/lib64:$LD_LIBRARY_PATH:/usr/local/cuda/lib64:/usr/local/lib
ENV PATH=${GCC7_DIR}/bin:$PATH

# Enables "source activate conda"
SHELL ["/bin/bash", "-c"]

# Install custom packages
RUN yum -y install rpm-build \
        screen \
        vim \
        zlib-devel \
        bzip2-devel \
        xz-devel \
        libcurl-devel \
        wget \
        # VariantWorks `cyvcf2` dependency
        libssl-dev \
        # cmake3 dependency
        openssl-devel \
	    # samtools dependency
	    ncurses-devel

# Add a condarc for channels and override settings
RUN echo -e "\
ssl_verify: False \n\
channels: \n\
  - gpuci \n\
  - conda-forge \n\
  - nvidia \n\
  - defaults \n" > /conda/.condarc \
      && cat /conda/.condarc ;

# Create `parabricks` conda env and make default
RUN source activate base \
    && conda install -y gpuci-tools \
    && gpuci_conda_retry create --no-default-packages --override-channels -n parabricks \
      -c nvidia \
      -c conda-forge \
      -c defaults \
      -c gpuci \
      -c bioconda \
      autoconf \
      cudatoolkit=${CUDA_VER} \
      git \
      gpuci-tools \
      htslib \
      python=${PYTHON_VERSION} \
      rsync \
      "setuptools<50" \
      && sed -i 's/conda activate base/conda activate parabricks/g' ~/.bashrc

# Install gcc7 from prebuilt tarball
RUN gpuci_retry wget --quiet ${CENTOS7_GCC7_URL} -O /gcc7.tgz \
    && tar xzvf /gcc7.tgz \
    && rm -f /gcc7.tgz

# Install cmake3
RUN wget https://github.com/Kitware/CMake/releases/download/v3.18.3/cmake-3.18.3.tar.gz \
    && tar zxvf cmake-3.* \
    && rm -rf cmake-3*.tar.gz \
    && cd cmake-3.* \
    && ./bootstrap --prefix=/usr/local \
    && make -j16 \
    && make install

# Install samtools
RUN wget https://github.com/samtools/samtools/releases/download/1.12/samtools-1.12.tar.bz2 && \
    tar -xf samtools-1.12.tar.bz2  && \
    cd  samtools-1.12 && \
    ./configure && make && make install

# Create symlink for old scripts expecting `gdf` conda env
RUN ln -s /opt/conda/envs/parabricks /opt/conda/envs/gdf

# Clean up pkgs to reduce image size and chmod for all users
RUN conda clean -afy \
    && chmod -R ugo+w /opt/conda

ENTRYPOINT [ "/usr/bin/tini", "--" ]
CMD [ "/bin/bash" ]