mirror of
https://github.com/KosinskiLab/AlphaPulldown.git
synced 2026-06-04 22:34:26 +08:00
fc41c1a5eb
- Strip _entity_poly_seq from generated template mmCIF so AF3 reconstructs _pdbx_poly_seq_scheme from _atom_site, avoiding UNK/gap mismatches - Build query_to_template_map using only residues with atoms to prevent OOB indexing in template features - Add --debug_templates flag to optionally dump generated template mmCIFs into templates_debug/ - Keep templates enabled; test test__chopped_dimer now passes
81 lines
2.7 KiB
Docker
81 lines
2.7 KiB
Docker
FROM nvidia/cuda:12.6.0-base-ubuntu22.04
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# ---------------------------------------------------------
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# 1. System Packages Installation
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# ---------------------------------------------------------
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RUN apt-get update -q && \
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DEBIAN_FRONTEND=noninteractive apt-get install -y -q --no-install-recommends \
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software-properties-common \
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git \
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wget \
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gcc \
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g++ \
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make \
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zlib1g-dev \
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zstd \
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&& rm -rf /var/lib/apt/lists/*
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# ---------------------------------------------------------
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# 2. Miniforge Installation
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# ---------------------------------------------------------
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RUN wget -q -P /tmp https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh && \
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bash /tmp/Miniforge3-Linux-x86_64.sh -b -p /opt/conda && \
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rm /tmp/Miniforge3-Linux-x86_64.sh
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ENV PATH="/opt/conda/bin:$PATH"
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ENV LD_LIBRARY_PATH="/opt/conda/lib:$LD_LIBRARY_PATH"
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# ---------------------------------------------------------
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# 3. Conda + Mamba Environment
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# ---------------------------------------------------------
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RUN conda install --solver=classic -y \
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conda-forge::conda-libmamba-solver \
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conda-forge::libmamba \
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conda-forge::libmambapy \
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conda-forge::libarchive \
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conda-forge::git && \
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mamba install -y -c conda-forge -c bioconda -c omnia --solver classic \
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openmm==8.0 \
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pdbfixer==1.9 \
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kalign2 \
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modelcif \
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pip \
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hmmer \
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hhsuite \
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python=3.11 && \
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conda clean --all --force-pkgs-dirs --yes
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# ---------------------------------------------------------
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# 4. Clone AlphaPulldown & Install
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# ---------------------------------------------------------
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RUN git clone --recurse-submodules https://github.com/KosinskiLab/AlphaPulldown.git
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WORKDIR /AlphaPulldown
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RUN pip3 install .
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# ---------------------------------------------------------
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# 5. Additional Python Tools
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# ---------------------------------------------------------
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RUN pip3 install --upgrade pip --no-cache-dir && \
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pip3 install --upgrade --no-cache-dir \
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pytest \
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"jax[cuda12]" && \
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chmod u+s /sbin/ldconfig.real
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# ---------------------------------------------------------
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# 6. AlphaFold 3 Source & Dependencies
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# ---------------------------------------------------------
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COPY alphafold3/ /app/alphafold3
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WORKDIR /app/alphafold3
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RUN pip3 install -r dev-requirements.txt && \
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pip3 install --no-deps . && \
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build_data
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# ---------------------------------------------------------
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# 7. Environment for XLA
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# ---------------------------------------------------------
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ENV XLA_FLAGS="--xla_gpu_enable_triton_gemm=false"
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ENV XLA_PYTHON_CLIENT_PREALLOCATE=true
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ENV XLA_CLIENT_MEM_FRACTION=0.95
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ENTRYPOINT ["bash"]
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