Dockerfile.template

# :Author: Jonathan Karr <karr@mssm.edu>
# :Date: 2018-08-28
# :Copyright: 2017-2018, Karr Lab
# :License: MIT

# base
FROM ubuntu

# upgrade
RUN apt-get update -y \
    && apt-get upgrade -y \
    && apt-get autoremove -y \
    && rm -rf /var/lib/apt/lists/*

# Create user to run operations in containers
RUN groupadd -r -g 999 container_user \
    && useradd -m -r -u 999 -g container_user container_user

# set time zone
ARG timezone=America/New_York
RUN apt-get update -y \
    && apt-get install -y --no-install-recommends tzdata \
    && rm -rf /var/lib/apt/lists/* \
    && ln -fs /usr/share/zoneinfo/$timezone /etc/localtime \
    && dpkg-reconfigure -f noninteractive tzdata

# set locale
RUN apt-get update -y \
    && apt-get install -y --no-install-recommends \
        locales \
    && rm -rf /var/lib/apt/lists/* \
    && locale-gen en_US.UTF-8
ENV LC_ALL=en_US.UTF-8

# install utilities: Git, SSH
RUN apt-get update -y \
    && apt-get install -y --no-install-recommends \
        git \
        ssh \
    && rm -rf /var/lib/apt/lists/*

# install Python
ARG python_version=3.6.5
ARG python_version_major_minor=3.6
ENV LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/local/lib
RUN apt-get update -y \
    && apt-get install -y --no-install-recommends \
        build-essential \
        ca-certificates \
        libbz2-dev \
        libexpat1 \
        libexpat1-dev \
        libffi-dev \
        libffi6 \
        libreadline-dev \
        libsqlite3-dev \
        libssl-dev \
        tar \
        tk-dev \
        wget \
        zlib1g-dev \
        # libdb5.3-dev # Berkeley DB \
        # libgdbm-dev # GNU dbm database \
        # liblzma-dev # LZMA compression \
        # libncursesw-dev # text-based user interfaces \
        # libtinfo-dev # terminal information \
        # mime-support # MIME support \
    \
    && cd /tmp \
    && wget https://www.python.org/ftp/python/${python_version}/Python-${python_version}.tgz -O /tmp/Python-${python_version}.tgz \
    && tar xzf /tmp/Python-${python_version}.tgz \
    && cd /tmp/Python-${python_version} \
    && ./configure \
        --prefix=/usr/local \
        --enable-optimizations \
        --enable-shared \
        --enable-unicode=ucs4 \
        --with-system-expat \
        --with-system-ffi \
    && make \
    # && make test \
    && make install \
    && ldconfig \
    && python${python_version_major_minor} -m ensurepip \
    && cd / \
    && rm -r /tmp/Python-${python_version}.tgz \
    && rm -r /tmp/Python-${python_version} \
    \
    && apt-get remove -y \
        build-essential \
        ca-certificates \
        libbz2-dev \
        libexpat1-dev \
        libffi-dev \
        libreadline-dev \
        libsqlite3-dev \
        libssl-dev \
        tk-dev \
        wget \
        zlib1g-dev \
    && apt-get autoremove -y \
    && rm -rf /var/lib/apt/lists/*

# Java
{% if java_install -%}
RUN apt-get update -y \
    && apt-get install -y --no-install-recommends \
        default-jre \
    && rm -rf /var/lib/apt/lists/*
{%- endif %}

# install PostgreSQL client
{% if postgresql_client_install -%}
RUN apt-get update -y \
    && apt-get install -y --no-install-recommends \
        gnupg \
        wget \
    && ubuntu_version=`cat /etc/lsb-release | grep DISTRIB_CODENAME | cut -d "=" -f 2` \
    && wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | apt-key add - \
    && echo "deb http://apt.postgresql.org/pub/repos/apt/ ${ubuntu_version}-pgdg main" >> /etc/apt/sources.list.d/pgdg_${ubuntu_version}.list \
    && apt-get update -y \
    && apt-get install -y --no-install-recommends \
        postgresql-client-10 \
    \
    && apt-get remove -y \
        gnupg \
        wget \
    && apt-get autoremove -y \
    && rm -rf /var/lib/apt/lists/*
{%- endif %}

# install openbabel
{% if openbabel_install -%}
ARG openbabel_version=2.4.1
RUN apt-get update -y \
    && apt-get install -y --no-install-recommends \
        build-essential \
        cmake \
        libcairo2-dev \
        libeigen3-dev \
        libxml2-dev \
        tar \
        wget \
        zlib1g-dev \
    \
    && cd /tmp \
    && openbabel_version_dash=$(echo $openbabel_version | sed 's/\./-/g') \
    && wget https://github.com/openbabel/openbabel/archive/openbabel-${openbabel_version_dash}.tar.gz -O /tmp/openbabel-${openbabel_version}.tar.gz \
    && tar -xvvf /tmp/openbabel-${openbabel_version}.tar.gz \
    && cd openbabel-openbabel-${openbabel_version_dash} \
    && mkdir build \
    && cd build \
    && cmake .. \
    && make \
    # && make test \
    && make install \
    && ldconfig \
    && cd / \
    && rm -r /tmp/openbabel-${openbabel_version}.tar.gz \
    && rm -r /tmp/openbabel-openbabel-${openbabel_version_dash} \
    \
    && apt-get remove -y \
        build-essential \
        cmake \
        libcairo2-dev \
        libeigen3-dev \
        libxml2-dev \
        wget \
        zlib1g-dev \
    && apt-get autoremove -y \
    && rm -rf /var/lib/apt/lists/*
{%- endif %}

# install cplex
{% if cplex_install -%}
ARG cplex_version=12.8.0
ARG cplex_version_major_minor_nodot=128
COPY cplex_studio${cplex_version_major_minor_nodot}.linux-x86-64.bin /tmp/
COPY cplex.installer.properties /tmp/
RUN apt-get update -y \
    && apt-get install -y --no-install-recommends \
        unzip \
    \
    && cd /tmp \
    && ./cplex_studio${cplex_version_major_minor_nodot}.linux-x86-64.bin \
        -f /tmp/cplex.installer.properties \
    \
    && cd /opt/ibm/ILOG/CPLEX_Studio${cplex_version_major_minor_nodot}/cplex/python/3.6/x86-64_linux/ \
    && pip${python_version_major_minor} install . \
    \
    && rm /tmp/cplex_studio${cplex_version_major_minor_nodot}.linux-x86-64.bin \
    && rm /tmp/cplex.installer.properties \
    \
    && apt-get remove -y \
        unzip \
    && apt-get autoremove -y \
    && rm -rf /var/lib/apt/lists/*
{%- endif %}

# install gurobi
{% if gurobi_install -%}
ARG gurobi_version=8.0.1
ARG gurobi_license={{ gurobi_license }}
COPY install_gurobi.exp /tmp/
RUN apt-get update -y \
    && apt-get install -y --no-install-recommends \
        expect \
        tar \
        wget \
    \
    && cd /tmp \
    && gurobi_version_major=$(echo $gurobi_version | cut -d "." -f 1,2) \
    && gurobi_version_nodot=$(echo $gurobi_version | sed 's/\.//g') \
    && wget http://packages.gurobi.com/${gurobi_version_major}/gurobi${gurobi_version}_linux64.tar.gz \
    && tar xvfz gurobi${gurobi_version}_linux64.tar.gz \
    && mv gurobi${gurobi_version_nodot} /opt/ \
    && /tmp/install_gurobi.exp "${gurobi_version_nodot}" "${gurobi_license}" \
    && cd /opt/gurobi${gurobi_version_nodot}/linux64 \
    && python${python_version_major_minor} setup.py install \
    && rm /tmp/gurobi${gurobi_version}_linux64.tar.gz \
    && rm /tmp/install_gurobi.exp \
    \
    && apt-get remove -y \
        expect \
        wget \
    && apt-get autoremove -y \
    && rm -rf /var/lib/apt/lists/*
ARG gurobi_version_nodot=800
ENV GUROBI_HOME=/opt/gurobi${gurobi_version_nodot}/linux64 \
    PATH="${PATH}:${GUROBI_HOME}/bin" \
    LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${GUROBI_HOME}/lib"
{%- endif %}

# install mosek
{% if mosek_install -%}
ARG mosek_version=8.1.0.58
COPY {{ mosek_license }} /tmp/
RUN apt-get update -y \
    && apt-get install -y --no-install-recommends \
        tar \
        wget \
    \
    && cd /tmp \
    && mosek_version_major=$(echo $mosek_version | cut -d "." -f 1,1) \
    && wget https://d2i6rjz61faulo.cloudfront.net/stable/${mosek_version}/mosektoolslinux64x86.tar.bz2 \
    && tar -xvvf mosektoolslinux64x86.tar.bz2 \
    && mv /tmp/mosek /opt/ \
    && mkdir ${HOME}/mosek \
    && mv /tmp/{{ mosek_license }} ${HOME}/mosek/ \
    && cd /opt/mosek/8/tools/platform/linux64x86/python/3/ \
    && python${python_version_major_minor} setup.py install \
    && rm /tmp/mosektoolslinux64x86.tar.bz2 \
    && rm ${HOME}/mosek/{{ mosek_license }} \
    \
    && apt-get remove -y \
        wget \
    && apt-get autoremove -y \
    && rm -rf /var/lib/apt/lists/*
ENV PATH="${PATH}:/opt/mosek/${mosek_version_major}/tools/platform/linux64x86/bin" \
    LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/opt/mosek/${mosek_version_major}/tools/platform/linux64x86/bin"
{%- endif %}

# install xpress
{% if xpress_install -%}
ARG xpress_version=8.5.3
ARG xpress_license_server={{ xpress_license_server }}
COPY {{ xpress_license }} /tmp/
COPY xpress.egg-info /tmp/
RUN apt-get update -y \
    && apt-get install -y --no-install-recommends \
        tar \
        wget \
    \
    && cd /tmp \
    && wget https://clientarea.xpress.fico.com/downloads/${xpress_version}/xp${xpress_version}_linux_x86_64_setup.tar \
    && mkdir xp${xpress_version}_linux_x86_64_setup \
    && tar -xvvf xp${xpress_version}_linux_x86_64_setup.tar -C xp${xpress_version}_linux_x86_64_setup \
    && cd /tmp/xp${xpress_version}_linux_x86_64_setup \
    && ./install.sh -l floating-client -a /tmp/{{ xpress_license }} -d /opt/xpressmp -k yes -s ${xpress_license_server} \
    && echo "/opt/xpressmp/lib" | tee /usr/local/lib/python${python_version_major_minor}/site-packages/xpress.pth \
    && cp /tmp/xpress.egg-info /usr/local/lib/python${python_version_major_minor}/site-packages/xpress-${xpress_version}.egg-info \
    && cd /tmp \
    && rm /tmp/xp${xpress_version}_linux_x86_64_setup.tar \
    && rm -r /tmp/xp${xpress_version}_linux_x86_64_setup \
    && rm /tmp/{{ xpress_license }} \
    && rm /tmp/xpress.egg-info \
    && rm /opt/xpressmp/bin/{{ xpress_license }} \
    \
    && apt-get remove -y \
        wget \
    && apt-get autoremove -y \
    && rm -rf /var/lib/apt/lists/*
ENV XPRESSDIR=/opt/xpressmp \
    PATH=$PATH:$XPRESSDIR/bin \
    LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/lib/x86_64-linux-gnu:$XPRESSDIR/lib \
    CLASSPATH=$CLASSPATH:$XPRESSDIR/lib/xprs.jar:$XPRESSDIR/lib/xprb.jar:$XPRESSDIR/lib/xprm.jar \
    XPRESS=$XPRESSDIR/bin
{%- endif %}

# COIN-OR: CBC (latest version compatible with CyLP)
{% if cbc_install -%}
ARG cbc_version=2.8.5
RUN apt-get update -y \
    && apt-get install -y --no-install-recommends \
        build-essential \
        tar \
        wget \
    \
    && cd /tmp \
    && wget https://www.coin-or.org/download/source/Cbc/Cbc-${cbc_version}.tgz \
    && tar -xvvf Cbc-${cbc_version}.tgz \
    && cd Cbc-${cbc_version} \
    && mkdir build \
    && cd build \
    && mkdir -p /opt/coin-or/cbc \
    && ../configure -C --prefix=/opt/coin-or/cbc --enable-gnu-packages \
    && make \
    # && make test \
    && make install \
    && cd ../../ \
    && rm -r Cbc-${cbc_version} \
    && rm Cbc-${cbc_version}.tgz \
    \
    && apt-get remove -y \
        build-essential \
        wget \
    && apt-get autoremove -y \
    && rm -rf /var/lib/apt/lists/*
ENV COIN_INSTALL_DIR=/opt/coin-or/cbc \
    PATH=${PATH}:/opt/coin-or/cbc/bin \
    LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/opt/coin-or/cbc/lib
{%- endif %}

# COIN-OR: coinutils
{% if coin_utils_install -%}
ARG coin_utils_version=2.10.14
RUN apt-get update -y \
    && apt-get install -y --no-install-recommends \
       build-essential \
       tar \
       wget \
    \
    && cd /tmp \
    && wget https://www.coin-or.org/download/source/CoinUtils/CoinUtils-${coin_utils_version}.tgz \
    && tar -xvvf CoinUtils-${coin_utils_version}.tgz \
    && cd CoinUtils-${coin_utils_version} \
    && mkdir build \
    && cd build \
    && mkdir -p /opt/coin-or/coinutils \
    && ../configure -C --prefix=/opt/coin-or/coinutils --enable-gnu-packages \
    && make \
    # && make test \
    && make install \
    && cd /tmp \
    && rm -r CoinUtils-${coin_utils_version} \
    && rm CoinUtils-${coin_utils_version}.tgz \
    \
    && apt-get remove -y \
       build-essential \
       wget \
    && apt-get autoremove -y \
    && rm -rf /var/lib/apt/lists/*
ENV PATH=${PATH}:/opt/coin-or/coinutils/bin \
    LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/opt/coin-or/coinutils/lib
{%- endif %}

# install qpOASES
{% if qpoases_install -%}
ARG qpoases_version=3.2.1
RUN apt-get update -y \
    && apt-get install -y --no-install-recommends \
      build-essential \
      tar \
      wget \
    \
    && cd /tmp \
    && wget https://www.coin-or.org/download/source/qpOASES/qpOASES-${qpoases_version}.tgz \
    && tar -xvvf qpOASES-${qpoases_version}.tgz \
    && cd qpOASES-${qpoases_version} \
    && make \
    # && make test \
    && mkdir -p /opt/coin-or/qpoases/lib \
    && cp bin/libqpOASES.* /opt/coin-or/qpoases/lib \
    && cp -r include/ /opt/coin-or/qpoases \
    && cd interfaces/python \
    && pip${python_version_major_minor} install cython numpy \
    && python${python_version_major_minor} setup.py install \
    && cd /tmp \
    && rm -r qpOASES-${qpoases_version} \
    && rm qpOASES-${qpoases_version}.tgz \
    \
    && apt-get remove -y \
      build-essential \
      wget \
    && apt-get autoremove -y \
    && rm -rf /var/lib/apt/lists/*
ENV LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/opt/coin-or/qpoases/lib
{%- endif %}

# MINOS
{% if minos_install -%}
ARG minos_version=5.6
RUN cd /tmp \
    && apt-get update -y \
    && apt-get install -y --no-install-recommends \
        csh \
        gfortran \
        git \
        make \
        wget \
        unzip \
    \
    && pip${python_version_major_minor} install numpy \
    && wget http://stanford.edu/~saunders/tmp/quadLP.zip \
    && unzip quadLP.zip \
    \
    && cd /tmp/quadLP/minos56 \
    && sed -i 's/FC        = gfortran/FC        = gfortran -fPIC/g' Makefile.defs \
    && make clean \
    && make \
    && cd /tmp/quadLP/minos56/test \
    && make minos \
    # && ./run minos t1diet \
    \
    && cd /tmp/quadLP/qminos56 \
    && sed -i 's/FC        = gfortran/FC        = gfortran -fPIC/g' Makefile.defs \
    && make clean \
    && make \
    && cd /tmp/quadLP/qminos56/test \
    && make minos \
    # && ./run minos t1diet \
    \
    && cd /tmp \
    && git clone https://github.com/SBRG/solvemepy.git \
    && cd solvemepy \
    && git checkout 72db1bac4ee8a479283f54eaf1644119967d4ac0 \
    && cp /tmp/quadLP/minos56/lib/libminos.a ./ \
    && cp /tmp/quadLP/qminos56/lib/libquadminos.a ./ \
    && pip${python_version_major_minor} install . \
    \
    && cd /tmp \
    && rm -r quadLP  \
    && rm quadLP.zip \
    && rm -r solvemepy \
    \
    && apt-get remove -y \
        csh \
        make \
        wget \
        unzip \
    && apt-get autoremove -y \
    && rm -rf /var/lib/apt/lists/*
{%- endif %}

# SoPlex
{% if soplex_install -%}
ARG soplex_version=3.1.1
RUN apt-get update -y \
    && apt-get install -y --no-install-recommends \
        build-essential \
        cmake \
        tar \
        wget \
    \
    && cd /tmp \
    && wget http://soplex.zib.de/download/release/soplex-${soplex_version}.tgz \
    && tar -xvvf soplex-${soplex_version}.tgz \
    && cd soplex-${soplex_version} \
    && mkdir build \
    && cd build \
    && cmake .. \
    && make \
    # && make test \
    && make install \
    && cd /tmp \
    && rm -r soplex-${soplex_version}  \
    && rm soplex-${soplex_version}.tgz  \
    \
    && apt-get install -y --no-install-recommends \
        libgmp-dev \
    \
    && pip${python_version_major_minor} install cython \
    && cd /tmp \
    && git clone https://github.com/SBRG/soplex_cython.git \
    && cd soplex_cython \
    && wget http://soplex.zib.de/download/release/soplex-${soplex_version}.tgz \
    && pip${python_version_major_minor} install . \
    && cd /tmp \
    && rm -r soplex_cython \
    \
    && apt-get remove -y \
        build-essential \
        cmake \
        libgmp-dev \
        wget \
    && apt-get autoremove -y \
    && rm -rf /var/lib/apt/lists/*
{%- endif %}

# kallisto
{% if kallisto_install -%}
ARG kallisto_version=0.44.0
RUN apt-get update -y \
    && apt-get install -y --no-install-recommends \
        tar \
        wget \
    \
    && cd /tmp \
    && wget https://github.com/pachterlab/kallisto/releases/download/v${kallisto_version}/kallisto_linux-v${kallisto_version}.tar.gz \
    && tar -xvvf kallisto_linux-v${kallisto_version}.tar.gz \
    && cp kallisto_linux-v${kallisto_version}/kallisto /usr/local/bin \
    && rm -rf kallisto_linux-v${kallisto_version} \
    && rm -rf kallisto_linux-v${kallisto_version}.tar.gz \
    \
    && apt-get remove -y \
        wget \
    && apt-get autoremove -y \
    && rm -rf /var/lib/apt/lists/*
{%- endif %}

# Docker
{% if docker_install -%}
RUN apt-get update -y \
    && apt-get install -y --no-install-recommends \
        apt-transport-https \
        ca-certificates \
        curl \
        software-properties-common \
    && curl -fsSL https://download.docker.com/linux/ubuntu/gpg | apt-key add - \
    && add-apt-repository \
        "deb [arch=amd64] https://download.docker.com/linux/ubuntu \
        $(lsb_release -cs) \
        stable" \
    \
    && apt-get update -y \
    && apt-get install -y --no-install-recommends docker-ce \
    && rm -rf /var/lib/apt/lists/*
{%- endif %}

# CircleCI local build agent
{% if circleci_install -%}
RUN curl -o /usr/local/bin/circleci https://circle-downloads.s3.amazonaws.com/releases/build_agent_wrapper/circleci \
    && chmod +x /usr/local/bin/circleci
{%- endif %}

# Install Python packages; pbr has to be installed first to workaround error in sphinxcontrib-spelling installation
COPY requirements.txt /tmp/
RUN apt-get update -y \
    && apt-get install -y --no-install-recommends \
        build-essential \
        default-libmysqlclient-dev \
        enchant \
        graphviz \
        pandoc \
        swig \
    \
    && pip${python_version_major_minor} install -U pip setuptools \
    && pip${python_version_major_minor} install -U \
        cython \
        ipython \
        mock \
        numpy \
        pbr \
        pypandoc \
        requests \
        six \
    && pip${python_version_major_minor} install -U git+https://github.com/jjhelmus/CyLP.git@py3#egg=cylp \
    && pip${python_version_major_minor} install -r /tmp/requirements.txt \
    && rm tmp/requirements.txt \
    \
    && apt-get remove -y \
        build-essential \
        swig \
    && apt-get autoremove -y \
    && rm -rf /var/lib/apt/lists/*

# Install NCBI taxonomy database and ETE3 package
RUN pip${python_version_major_minor} install ete3 \
    && python${python_version_major_minor} -c "import ete3; ete3.NCBITaxa().get_descendant_taxa('Homo');" \
    && rm /taxdump.tar.gz

# Save image tag to file so it is accessible from within containers
ARG image_tag={{ image_tag }}
RUN echo ${image_tag} > /etc/docker-image-tag

# install debugging utilities
# RUN apt-get update -y \
#    && apt-get install -y --no-install-recommends \
#       nano \
#       postgresql \
#       snapd \
#    && snap install pycharm-community --classic \
#    && rm -rf /var/lib/apt/lists/*

# cleanup
# RUN apt-get remove -y \
#       build-essential \
#       cmake

# final command
WORKDIR /root
CMD bash