Dockerfile-base

#############
### base ###
#############
FROM python:3.9-slim-buster

LABEL \
    org.opencontainers.image.title="BioSimulators-base" \
    org.opencontainers.image.description="Docker image the dependencies for the simulation tools registered BioSimulators" \
    org.opencontainers.image.url="https://biosimulators.org/" \
    org.opencontainers.image.documentation="https://docs.biosimulations.org/" \
    org.opencontainers.image.source="https://github.com/biosimulators/Biosimulators" \
    org.opencontainers.image.authors="BioSimulators Team <info@biosimulators.org>" \
    org.opencontainers.image.vendor="BioSimulators Team"

WORKDIR /app

###################################
# update apt package database
RUN apt-get update -y

###################################
# AMICI
RUN apt-get install --no-install-recommends -y \
        g++ \
        libatlas-base-dev \
        swig

###################################
# BioNetGen
ARG BIONETGEN_VERSION=2.8.0
RUN apt-get install -y --no-install-recommends \
        perl \
        tar \
        wget \
    \
    && cd /tmp \
    && wget https://github.com/RuleWorld/bionetgen/releases/download/BioNetGen-${BIONETGEN_VERSION}/BioNetGen-${BIONETGEN_VERSION}-linux.tgz \
    && tar xvvf BioNetGen-${BIONETGEN_VERSION}-linux.tgz \
    && mv BioNetGen-${BIONETGEN_VERSION}/ /opt/ \
    \
    && rm BioNetGen-${BIONETGEN_VERSION}-linux.tgz
ENV PATH=${PATH}:/opt/BioNetGen-${BIONETGEN_VERSION}/

###################################
# BoolNet
ARG BOOLNET_VERSION=2.1.5
RUN apt-get install -y --no-install-recommends \
        r-base \
        build-essential \
        gcc \
        gfortran \
        libblas-dev \
        libcurl4-openssl-dev \
        libgit2-dev \
        liblapack-dev \
        libssl-dev \
        libxml2 \
        libxml2-dev \
    \
    && Rscript \
        -e "install.packages('devtools')" \
        -e "require(devtools)" \
        -e "install_version('BoolNet', version='${BOOLNET_VERSION}')" \
        -e "require('BoolNet')"

###################################
# CBMPy
RUN apt-get install -y --no-install-recommends \
        gcc \
        libglpk-dev

###################################
# COBRAPY
RUN mkdir -p /.cache/cobrapy \
    && chmod ugo+rw /.cache/cobrapy

###################################
# COPASI

###################################
# GillesPy2
RUN apt-get install -y --no-install-recommends \
        build-essential

###################################
# GINsim
RUN mkdir -p /usr/share/man/man1/ \
    && apt-get install -y --no-install-recommends \
        default-jre \
        wget \
    \
    && cd /tmp \
    && pip install ginsim \
    && wget https://raw.githubusercontent.com/GINsim/GINsim-python/master/ginsim_setup.py \
    && python ginsim_setup.py \
    \
    && rm ginsim_setup.py

###################################
# libSBMLSIM
ARG LSBMLSIM_VERSION=1.4.0
ARG LIBSBML_VERSION=5.19.0

# libSBML
RUN apt-get install --no-install-recommends -y \
        wget \
        libxml2 \
    \
    && wget https://master.dl.sourceforge.net/project/sbml/libsbml/${LIBSBML_VERSION}/stable/Linux/64-bit/libSBML-${LIBSBML_VERSION}-Linux-x64.deb \
    && dpkg -i libSBML-${LIBSBML_VERSION}-Linux-x64.deb \
    \
    && rm libSBML-${LIBSBML_VERSION}-Linux-x64.deb
ENV LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH

# LibSBMLSim
RUN apt-get install --no-install-recommends -y \
        wget \
        build-essential \
        cmake \
        swig \
        libbz2-dev \
    \
    && PY_EXEC_PATH=$(which python) \
    && PY_PREFIX=$(echo ${PY_EXEC_PATH} | rev | cut -d "/" -f 3- | rev) \
    && cd /tmp \
    && wget https://github.com/libsbmlsim/libsbmlsim/archive/refs/tags/v${LSBMLSIM_VERSION}.tar.gz \
    && tar xvvf v${LSBMLSIM_VERSION}.tar.gz \
    && cd libsbmlsim-${LSBMLSIM_VERSION} \
    && mkdir build \
    && cd build \
    && PYTHON_MAJOR_MINOR_VERSION=$(echo $PYTHON_VERSION | cut -d . -f 1-2) \
    && cmake \
        -D LIBSBML_INCLUDE_DIR=/usr/include \
        -D LIBSBML_LIBRARY=/usr/lib64/libsbml.so \
        -D WITH_PYTHON=ON \
        -D PYTHON_PREFIX=${PY_PREFIX} \
        -D PYTHON_EXECUTABLE:FILEPATH=${PY_EXEC_PATH} \
        -D PYTHON_INCLUDE_DIR:PATH=/usr/local/include/python${PYTHON_MAJOR_MINOR_VERSION} \
        -D PYTHON_LIBRARY:FILEPATH=/usr/local/lib/libpython${PYTHON_MAJOR_MINOR_VERSION}.so \
        .. \
    \
    && make \
    && make install \
    \
    && cd /tmp \
    && rm v${LSBMLSIM_VERSION}.tar.gz \
    && rm -r libsbmlsim-${LSBMLSIM_VERSION}

###################################
# MASSpy
RUN apt-get install -y --no-install-recommends \
        git \
        gcc \
        build-essential \
        libfreetype6-dev \
        libfreetype6 \
        pkg-config \
    \
    && mkdir -p /.cache/cobrapy

###################################
# NetPyNe
RUN apt-get install -y --no-install-recommends \
    gcc \
    g++ \
    make \
    libmpich-dev \
    mpi \
    mpi-default-bin \
    mpich

###################################
# NEURON
RUN apt-get install -y --no-install-recommends \
    gcc \
    g++ \
    make
RUN pip install neuron
ENV NEURON_HOME=/usr/local

###################################
# pyNeuroML, LEMS
RUN mkdir -p /usr/share/man/man1/ \
    && apt-get install -y --no-install-recommends \
        default-jre

###################################
# PySCeS

# SUNDIALS
# ignore certificate checking because certificate was expired as of 2021-11-10
ARG SUNDIALS_VERSION=2.6.2
RUN apt-get install -y --no-install-recommends \
        wget \
        cmake \
        make \
        g++ \
    \
    && cd /tmp \
    && wget --no-check-certificate https://computing.llnl.gov/sites/default/files/inline-files/sundials-${SUNDIALS_VERSION}.tar.gz \
    && tar xvvf sundials-${SUNDIALS_VERSION}.tar.gz \
    && cd sundials-${SUNDIALS_VERSION} \
    && mkdir build \
    && cd build \
    && cmake .. \
    && make \
    && make install \
    \
    && cd /tmp \
    && rm sundials-${SUNDIALS_VERSION}.tar.gz \
    && rm -r sundials-${SUNDIALS_VERSION}
ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH

# Assimulo
RUN apt-get install -y --no-install-recommends \
        g++ \
        gfortran \
        libblas-dev \
        liblapack-dev \
        git

# PySCeS
RUN apt-get install -y --no-install-recommends \
        git \
        gcc \
        gfortran \
        libgfortran5

# Configure PySCeS
COPY .pys_usercfg.ini /Pysces/.pys_usercfg.ini
COPY .pys_usercfg.ini /root/Pysces/.pys_usercfg.ini
RUN mkdir -p /Pysces \
    && mkdir -p /Pysces/psc \
    && mkdir -p /root/Pysces \
    && mkdir -p /root/Pysces/psc \
    && chmod ugo+rw -R /Pysces

###################################
# RBApy
RUN apt-get install -y --no-install-recommends \
        gcc \
        libglpk-dev

###################################
# Smoldyn

###################################
# tellurium
RUN apt-get install -y --no-install-recommends \
        libxml2 \
        libncurses5
ENV PLOTTING_ENGINE=matplotlib \
    PYTHONWARNINGS="ignore:The 'warn' parameter of use():UserWarning:tellurium.tellurium,ignore:Matplotlib is currently using agg:UserWarning:tellurium.plotting.engine_mpl"

###################################
# XPP
RUN apt-get install -y --no-install-recommends \
        wget \
        make \
        gcc \
        libx11-dev \
        libc6-dev \
        libx11-6 \
        libc6 \
    \
    && cd /tmp \
    && wget http://www.math.pitt.edu/~bard/bardware/xppaut_latest.tar.gz \
    && mkdir xpp \
    && tar zxvf xppaut_latest.tar.gz --directory xpp \
    && cd xpp \
    && make \
    && make install \
    \
    && cd /tmp \
    && rm xppaut_latest.tar.gz \
    && rm -r xpp

###################################
# setup headless for NEURON, Smoldyn
RUN apt-get -y update \
    \
    && apt-get install --no-install-recommends -y \
        xvfb \
    && mkdir /tmp/.X11-unix \
    && chmod 1777 /tmp/.X11-unix \
    \
    && rm -rf /var/lib/apt/lists/*
COPY xvfb-startup.sh /xvfb-startup.sh
ENV XVFB_RES="1920x1080x24" \
    XVFB_ARGS=""

###################################
# fonts for matplotlib
RUN apt-get update -y \
    && apt-get install -y --no-install-recommends libfreetype6 \
    && rm -rf /var/lib/apt/lists/*

# configure matplotlib cache and config to avoid warnings
RUN mkdir -p /.cache/matplotlib \
    && mkdir -p /.config/matplotlib \
    && chmod ugo+rw /.config/matplotlib \
    && chmod ugo+rw /.cache/matplotlib

# Configure default simulator options
ENV ALGORITHM_SUBSTITUTION_POLICY=SIMILAR_VARIABLES \
    VERBOSE=0 \
    MPLBACKEND=PDF \
    PLOTTING_ENGINE=matplotlib