mirror of https://github.com/exaloop/codon
53 lines
2.1 KiB
Docker
53 lines
2.1 KiB
Docker
FROM exaloop/codon-llvm:15.0.1
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ENV pass="codon-jupyter"
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# Install dependencies
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RUN yum -y install openssl-devel libsodium-devel libuuid-devel
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# Build Codon core
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RUN git clone -b develop https://github.com/exaloop/codon /github/codon
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RUN cmake3 -S /github/codon -B /github/codon/build \
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-G Ninja \
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-DCMAKE_BUILD_TYPE=Release \
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-DCMAKE_C_COMPILER=/opt/llvm-codon/bin/clang \
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-DCMAKE_CXX_COMPILER=/opt/llvm-codon/bin/clang++ \
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-DLLVM_DIR=/opt/llvm-codon/lib/cmake/llvm \
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-DCMAKE_INSTALL_PREFIX=/opt/codon
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RUN cmake3 --build /github/codon/build
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RUN cmake3 --install /github/codon/build
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# Build Codon Jupyter support
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RUN cmake3 -S /github/codon/jupyter -B /github/codon/jupyter/build \
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-G Ninja \
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-DCMAKE_BUILD_TYPE=Release \
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-DCMAKE_C_COMPILER=/opt/llvm-codon/bin/clang \
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-DCMAKE_CXX_COMPILER=/opt/llvm-codon/bin/clang++ \
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-DLLVM_DIR=/opt/llvm-codon/lib/cmake/llvm \
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-DCODON_PATH=/opt/codon \
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-DOPENSSL_ROOT_DIR=$(openssl version -d | cut -d' ' -f2 | tr -d '"') \
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-DOPENSSL_CRYPTO_LIBRARY=/usr/lib64/libssl.so \
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-DXEUS_USE_DYNAMIC_UUID=ON
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RUN cmake3 --build /github/codon/jupyter/build
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RUN cmake3 --install /github/codon/jupyter/build
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# Build Seq (bioinformatics plugin) for Codon
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RUN git clone -b develop https://github.com/exaloop/seq /github/seq
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RUN cmake3 -S /github/seq -B /github/seq/build \
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-G Ninja \
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-DCMAKE_BUILD_TYPE=Release \
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-DCMAKE_C_COMPILER=/opt/llvm-codon/bin/clang \
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-DCMAKE_CXX_COMPILER=/opt/llvm-codon/bin/clang++ \
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-DLLVM_DIR=/opt/llvm-codon/lib/cmake/llvm \
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-DCODON_PATH=/opt/codon
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RUN cmake3 --build /github/seq/build
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RUN cmake3 --install /github/seq/build
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# Set up Codon Jupyter kernel
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RUN pip3 install ipywidgets==7.6.5 numpy matplotlib pandas scipy jupyter plotly
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RUN mkdir -p /usr/share/jupyter/kernels/codon
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RUN echo '{"display_name": "Codon", "argv": [ "/opt/codon/bin/codon", "jupyter", "-plugin", "seq", "{connection_file}" ], "language": "python"}' > /usr/share/jupyter/kernels/codon/kernel.json
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# Launch Jupyter
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ENV CODON_PYTHON="/usr/lib64/libpython3.so"
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CMD jupyter notebook --port=8888 --no-browser --ip=0.0.0.0 --allow-root --NotebookApp.token=${pass}
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