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# 1. Download ChemAxon Marvin for Debian from https://chemaxon.com/ and save to ./Dockerfile_assets/marvin_linux.deb
# 2. Obtain license for Marvin and save to ./Dockerfile_assets/chemaxon.license.cxl
# 3. Build with `docker build -f Dockerfile Dockerfile_assets --tag karrlab/bpforms:latest`
# Start from Ubuntu (e.g., bionic - 18.04.4)
FROM ubuntu
# Set default language to UTF-8 US English
RUN apt-get update -y \
&& apt-get install --no-install-recommends -y \
locales \
&& rm -rf /var/lib/apt/lists/* \
&& locale-gen en_US.UTF-8
ENV LC_ALL=en_US.UTF-8
# Install Python (e.g., 3.6.9), pip, and setuptools
RUN apt-get update -y \
&& apt-get install --no-install-recommends -y \
python3 \
python3-pip \
&& pip3 install -U pip setuptools \
&& apt-get autoremove -y \
&& rm -rf /var/lib/apt/lists/*
# Install Open Babel 2.4.1
ARG openbabel_version=2.4.1
RUN apt-get update -y \
&& apt-get install --no-install-recommends -y \
build-essential \
cmake \
libcairo2-dev \
libeigen3-dev \
libxml2 \
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-${openbabel_version_dash} \
\
&& apt-get remove -y \
build-essential \
cmake \
libcairo2-dev \
libeigen3-dev \
libxml2-dev \
wget \
zlib1g-dev \
&& apt-get autoremove -y \
&& rm -rf /var/lib/apt/lists/*
# Install Open Babel Python interface
RUN apt-get update -y \
&& apt-get install --no-install-recommends -y \
build-essential \
libpython3-dev \
swig \
\
&& pip3 install openbabel \
\
&& apt-get remove -y \
build-essential \
libpython3-dev \
swig \
&& apt-get autoremove -y \
&& rm -rf /var/lib/apt/lists/*
# Install ChemAxon Marvin (e.g., 20.6)
COPY ./marvin_linux.deb /tmp/
COPY ./chemaxon.license.cxl /tmp/
RUN apt-get update -y \
&& apt-get install --no-install-recommends -y \
default-jdk \
default-jre \
\
&& mkdir ~/.chemaxon \
&& mv /tmp/chemaxon.license.cxl ~/.chemaxon/license.cxl \
&& dpkg -i /tmp/marvin_linux.deb \
\
&& rm /tmp/marvin_linux.deb \
&& apt-get autoremove -y \
&& rm -rf /var/lib/apt/lists/*
ENV JAVA_HOME=/usr/lib/jvm/default-java \
CLASSPATH=${CLASSPATH}:/opt/chemaxon/marvinsuite/lib/MarvinBeans.jar
# Install BcForms and BpForms
RUN pip3 install \
bcforms[draw] \
bpforms[draw,onto_export,protonation]
# Test installations of BcForms and BpForms
ARG test=1
RUN if [ "$test" = "1" ]; then \
apt-get update -y \
&& apt-get install --no-install-recommends -y \
git \
build-essential \
libpython3-dev \
\
&& cd / \
&& git clone https://github.com/KarrLab/bpforms.git \
&& git clone https://github.com/KarrLab/bcforms.git \
&& pip3 install pytest \
&& pip3 install -r bpforms/tests/requirements.txt \
&& pip3 install -r bcforms/tests/requirements.txt \
&& cd /bpforms \
&& python3 -m pytest tests/test_core.py tests/test_main.py \
&& cd /bcforms \
&& python3 -m pytest tests/test_core.py tests/test_main.py \
\
&& cd / \
&& rm -r bpforms \
&& rm -r bcforms \
&& apt-get remove -y \
git \
build-essential \
libpython3-dev \
&& apt-get autoremove -y \
&& rm -rf /var/lib/apt/lists/*; \
fi