mirror of
https://github.com/rdkit/rdkit.git
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b952b740d3
* Cannot push_back std::string to boost json array `boost::json::array.push_back` expects a `value` * prefer emplace_back to avoid casting * Ensure every MINIMAL_LIB option is tested in CI Also remove Chemdraw support from the compilation. This does not change the final size of the output (not exported anyways) but it reduces the compilation time by 1 min (-10% on my local machine) * Expose MMPA with other options * Fix MMPA compilation: Implicitly binding raw pointers is illegal Applying same pattern as in `get_frags_helper`
102 lines
4.7 KiB
Plaintext
102 lines
4.7 KiB
Plaintext
# Note: there are docker-compose .yml files that handle the 3
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# build steps automatically for you; see the comments in the
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# respective docker-compose files for details.
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# However, if you prefer to run individual docker commands rather
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# than using docker-compose, you can do so by following the
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# instructions below.
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#
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# Example usage of this Dockerfile:
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# (the --build-arg arguments are all optional)
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#
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# 1. cd to Code/MinimalLib/docker
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# cd Code/MinimalLib/docker
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#
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# 2. build the MinimalLib rdkit-minimallib-deps image:
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# docker build --target deps-stage -t rdkit-minimallib-deps \
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# --build-arg http_proxy=$HTTP_PROXY \
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# --build-arg https_proxy=$HTTP_PROXY \
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# --network=host --build-arg "EXCEPTION_HANDLING=-fwasm-exceptions" \
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# -f Dockerfile_1_deps .
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#
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# 3. build the MinimalLib rdkit-minimallib-rdkit-src image:
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# 3a. from a git clone:
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# docker build --target clone-stage -t rdkit-minimallib-rdkit-src \
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# --build-arg http_proxy=$HTTP_PROXY \
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# --build-arg https_proxy=$HTTP_PROXY \
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# --build-arg "RDKIT_GIT_URL=https://github.com/myfork/rdkit.git" \
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# --build-arg "RDKIT_BRANCH=mybranch" \
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# --network=host -f Dockerfile_rdkit_clone_from_github .
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# or
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# 3b. from an existing local source tree:
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# docker build --target local-src-stage -t rdkit-minimallib-rdkit-src \
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# --build-arg http_proxy=$HTTP_PROXY \
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# --build-arg https_proxy=$HTTP_PROXY \
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# --network=host -f Dockerfile_2_rdkit_copy_from_local ../../..
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#
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# 4. build the MinimalLib rdkit-minimallib image:
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# (the build-arg arguments are all optional; in the following
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# example we select the more performant, though still experimental,
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# native WASM exception handling):
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# docker build -t rdkit-minimallib --network=host \
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# --build-arg http_proxy=$HTTP_PROXY \
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# --build-arg https_proxy=$HTTP_PROXY \
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# --build-arg "EXCEPTION_HANDLING=-fwasm-exceptions" \
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# -f Dockerfile_3_rdkit_build .
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#
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# 5. create a temporary container and copy built libraries
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# from the container to your local filesystem, then destroy
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# the temporary container
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# docker create --name=rdkit-minimallib-container rdkit-minimallib:latest --entrypoint /
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# docker cp rdkit-minimallib-container:/RDKit_minimal.js ../demo
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# docker cp rdkit-minimallib-container:/RDKit_minimal.wasm ../demo
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# docker rm rdkit-minimallib-container
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ARG EXCEPTION_HANDLING="-fexceptions -sNO_DISABLE_EXCEPTION_CATCHING"
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FROM rdkit-minimallib-rdkit-src AS build-stage
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ARG EXCEPTION_HANDLING
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LABEL maintainer="Greg Landrum <greg.landrum@t5informatics.com>"
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WORKDIR /src
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ENV RDBASE=/src/rdkit
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RUN mkdir build
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WORKDIR $RDBASE/build
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RUN emcmake cmake -DRDK_BUILD_FREETYPE_SUPPORT=ON -DRDK_BUILD_MINIMAL_LIB=ON \
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-DRDK_BUILD_PYTHON_WRAPPERS=OFF -DRDK_BUILD_CPP_TESTS=OFF -DRDK_BUILD_INCHI_SUPPORT=ON \
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-DRDK_USE_BOOST_SERIALIZATION=OFF -DRDK_OPTIMIZE_POPCNT=OFF -DRDK_BUILD_THREADSAFE_SSS=OFF \
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-DRDK_BUILD_DESCRIPTORS3D=OFF -DRDK_TEST_MULTITHREADED=OFF \
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-DRDK_BUILD_CHEMDRAW_SUPPORT=OFF -DRDK_BUILD_MAEPARSER_SUPPORT=OFF -DRDK_BUILD_COORDGEN_SUPPORT=ON \
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-DRDK_BUILD_MINIMAL_LIB_MCS=ON -DRDK_BUILD_MINIMAL_LIB_MOLZIP=ON \
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-DRDK_BUILD_MINIMAL_LIB_MMPA=ON \
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-DBoost_DIR=/opt/boost/lib/cmake/Boost-${BOOST_DOT_VERSION} \
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-Dboost_headers_DIR=/opt/boost/lib/cmake/boost_headers-${BOOST_DOT_VERSION} \
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-DRDK_BUILD_SLN_SUPPORT=OFF -DRDK_USE_BOOST_IOSTREAMS=OFF \
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-DFREETYPE_INCLUDE_DIRS=/opt/freetype/include/freetype2 \
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-DFREETYPE_LIBRARY=/opt/freetype/lib/libfreetype.a \
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-DZLIB_INCLUDE_DIR=/opt/zlib/include \
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-DZLIB_LIBRARY=/opt/zlib/lib/libz.a \
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-DCMAKE_CXX_FLAGS="${EXCEPTION_HANDLING} -O3 -DNDEBUG" \
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-DCMAKE_C_FLAGS="${EXCEPTION_HANDLING} -O3 -DNDEBUG -DCOMPILE_ANSI_ONLY" \
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-DCMAKE_EXE_LINKER_FLAGS="${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'\"" ..
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# "patch" to make the InChI code work with emscripten:
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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 && \
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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
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# build and "install"
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RUN make -j2 RDKit_minimal && \
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cp Code/MinimalLib/RDKit_minimal.* ../Code/MinimalLib/demo/
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# run the tests
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WORKDIR /src/rdkit/Code/MinimalLib/tests
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RUN /opt/emsdk/node/*/bin/node tests.js
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# Copy js and wasm rdkit files to use in browser
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# This feature requires the BuildKit backend
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# https://docs.docker.com/engine/reference/commandline/build/#custom-build-outputs
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FROM scratch as export-stage
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COPY --from=build-stage /src/rdkit/Code/MinimalLib/demo /
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COPY --from=build-stage /src/rdkit/Code/MinimalLib/docs /
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