1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
|
# 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 RDKIT_GIT_URL="https://github.com/rdkit/rdkit.git"
ARG RDKIT_BRANCH="master"
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 RDKIT_GIT_URL
ARG RDKIT_BRANCH
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 /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
RUN git clone https://github.com/emscripten-core/emsdk.git
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 /src
ENV RDBASE=/src/rdkit
RUN git clone ${RDKIT_GIT_URL}
WORKDIR $RDBASE
RUN git fetch --all --tags && \
git checkout ${RDKIT_BRANCH}
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 /
|
