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# Example usage of this Dockerfile:
# (the build-arg arguments are all optional)
#
# 1. cd to Code/MinimalLib/docker
# cd Code/MinimalLib/docker
#
# 2. build the JS and WASM libraries
# (the build-arg arguments are all optional; in the following
# example we select the more performant, though still experimental,
# native WASM exception handling):
# docker build -t rdkit-minimallib --network=host \
# --build-arg "RDKIT_GIT_URL=https://github.com/myfork/rdkit.git" \
# --build-arg "RDKIT_BRANCH=mybranch" \
# --build-arg "EXCEPTION_HANDLING=-fwasm-exceptions".
#
# 3. create a temporary container and copy built libraries
# from the container to your local filesystem, then destroy
# the temporary container
# docker create --name=rdkit-minimallib-container rdkit-minimallib:latest --entrypoint /
# docker cp rdkit-minimallib-container:/RDKit_minimal.js ../demo
# docker cp rdkit-minimallib-container:/RDKit_minimal.wasm ../demo
# docker rm rdkit-minimallib-container
ARG EMSDK_VERSION="latest"
ARG EXCEPTION_HANDLING="-fexceptions -sNO_DISABLE_EXCEPTION_CATCHING"
ARG BOOST_MAJOR_VERSION="1"
ARG BOOST_MINOR_VERSION="87"
ARG BOOST_PATCH_VERSION="0"
ARG FREETYPE_VERSION="2.13.3"
FROM debian:bookworm AS build-stage
ARG EMSDK_VERSION
ARG EXCEPTION_HANDLING
ARG BOOST_MAJOR_VERSION
ARG BOOST_MINOR_VERSION
ARG BOOST_PATCH_VERSION
ARG FREETYPE_VERSION
LABEL maintainer="Greg Landrum <greg.landrum@t5informatics.com>"
RUN apt-get update && apt-get upgrade -y && apt install -y \
curl \
wget \
cmake \
python3 \
g++ \
libeigen3-dev \
git \
xz-utils \
nodejs
ENV LANG C
WORKDIR /opt
RUN git clone https://github.com/emscripten-core/emsdk.git
WORKDIR /src
ARG BOOST_DOT_VERSION="${BOOST_MAJOR_VERSION}.${BOOST_MINOR_VERSION}.${BOOST_PATCH_VERSION}"
ARG BOOST_UNDERSCORE_VERSION="${BOOST_MAJOR_VERSION}_${BOOST_MINOR_VERSION}_${BOOST_PATCH_VERSION}"
RUN wget -q https://archives.boost.io/release/${BOOST_DOT_VERSION}/source/boost_${BOOST_UNDERSCORE_VERSION}.tar.gz && \
tar xzf boost_${BOOST_UNDERSCORE_VERSION}.tar.gz
WORKDIR /src/boost_${BOOST_UNDERSCORE_VERSION}
RUN ./bootstrap.sh --prefix=/opt/boost --with-libraries=system && \
./b2 install
WORKDIR /opt/emsdk
RUN ./emsdk install ${EMSDK_VERSION} && \
./emsdk activate ${EMSDK_VERSION}
#RUN source ./emsdk_env.sh
RUN echo "source /opt/emsdk/emsdk_env.sh > /dev/null 2>&1" >> ~/.bashrc
SHELL ["/bin/bash", "-c", "-l"]
WORKDIR /src
RUN wget -q https://download.savannah.gnu.org/releases/freetype/freetype-${FREETYPE_VERSION}.tar.gz && \
tar xzf freetype-${FREETYPE_VERSION}.tar.gz
WORKDIR /src/freetype-${FREETYPE_VERSION}
RUN mkdir build
WORKDIR /src/freetype-${FREETYPE_VERSION}/build
RUN emcmake cmake -DCMAKE_BUILD_TYPE=Release -DWITH_ZLIB=OFF -DWITH_BZip2=OFF -DWITH_PNG=OFF \
-DCMAKE_C_FLAGS="${EXCEPTION_HANDLING}" -DCMAKE_EXE_LINKER_FLAGS="${EXCEPTION_HANDLING}" \
-DCMAKE_INSTALL_PREFIX=/opt/freetype ..
RUN make -j2 && make -j2 install
WORKDIR /
COPY Code /src/rdkit/Code
COPY External /src/rdkit/External
COPY CMakeLists.txt license.txt *.in *.md *.cmake /src/rdkit
ENV RDBASE=/src/rdkit
WORKDIR $RDBASE
RUN mkdir build
WORKDIR $RDBASE/build
RUN emcmake cmake -DRDK_BUILD_FREETYPE_SUPPORT=ON -DRDK_BUILD_MINIMAL_LIB=ON \
-DRDK_BUILD_PYTHON_WRAPPERS=OFF -DRDK_BUILD_CPP_TESTS=OFF -DRDK_BUILD_INCHI_SUPPORT=ON \
-DRDK_USE_BOOST_SERIALIZATION=OFF -DRDK_OPTIMIZE_POPCNT=OFF -DRDK_BUILD_THREADSAFE_SSS=OFF \
-DRDK_BUILD_DESCRIPTORS3D=OFF -DRDK_TEST_MULTITHREADED=OFF \
-DRDK_BUILD_MAEPARSER_SUPPORT=OFF -DRDK_BUILD_COORDGEN_SUPPORT=ON \
-DBoost_DIR=/opt/boost/lib/cmake/Boost-${BOOST_DOT_VERSION} \
-Dboost_headers_DIR=/opt/boost/lib/cmake/boost_headers-${BOOST_DOT_VERSION} \
-DRDK_BUILD_SLN_SUPPORT=OFF -DRDK_USE_BOOST_IOSTREAMS=OFF \
-DFREETYPE_INCLUDE_DIRS=/opt/freetype/include/freetype2 \
-DFREETYPE_LIBRARY=/opt/freetype/lib/libfreetype.a \
-DCMAKE_CXX_FLAGS="${EXCEPTION_HANDLING} -O3 -DNDEBUG" \
-DCMAKE_C_FLAGS="${EXCEPTION_HANDLING} -O3 -DNDEBUG -DCOMPILE_ANSI_ONLY" \
-DCMAKE_EXE_LINKER_FLAGS="${EXCEPTION_HANDLING} -s STACK_OVERFLOW_CHECK=1 -s USE_PTHREADS=0 -s ALLOW_MEMORY_GROWTH=1 -s MAXIMUM_MEMORY=4GB -s MODULARIZE=1 -s EXPORT_NAME=\"'initRDKitModule'\"" ..
# "patch" to make the InChI code work with emscripten:
RUN cp /src/rdkit/External/INCHI-API/src/INCHI_BASE/src/util.c /src/rdkit/External/INCHI-API/src/INCHI_BASE/src/util.c.bak && \
sed 's/&& defined(__APPLE__)//' /src/rdkit/External/INCHI-API/src/INCHI_BASE/src/util.c.bak > /src/rdkit/External/INCHI-API/src/INCHI_BASE/src/util.c
# comment out a line which causes a compilation error on some platforms
# (based on the change which has already been applied to the RapidJSON master branch, see
# https://github.com/Tencent/rapidjson/blob/ab1842a2dae061284c0a62dca1cc6d5e7e37e346/include/rapidjson/document.h#L414)
RUN sed -i 's|^\( *\)\(GenericStringRef\& operator=(const GenericStringRef\& rhs) { s = rhs.s; length = rhs.length; } *\)$|\1//\2|' \
/src/rdkit/External/rapidjson-1.1.0/include/rapidjson/document.h
# build and "install"
RUN make -j2 RDKit_minimal && \
cp Code/MinimalLib/RDKit_minimal.* ../Code/MinimalLib/demo/
# run the tests
WORKDIR /src/rdkit/Code/MinimalLib/tests
RUN /opt/emsdk/node/*/bin/node tests.js
# # Copy js and wasm rdkit files to use in browser
# # This feature requires the BuildKit backend
# # https://docs.docker.com/engine/reference/commandline/build/#custom-build-outputs
# FROM scratch AS export-stage
# COPY --from=build-stage /src/rdkit/Code/MinimalLib/demo /
# COPY --from=build-stage /src/rdkit/Code/MinimalLib/docs /
|
