97 lines
4.4 KiB
Docker
97 lines
4.4 KiB
Docker
FROM nvidia/cuda:12.1.0-cudnn8-runtime-ubuntu22.04
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# Set environment variables
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ENV DEBIAN_FRONTEND=noninteractive
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ENV PYTHONUNBUFFERED=1
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ENV PYTHONDONTWRITEBYTECODE=1
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# Set working directory
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WORKDIR /app
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# Install system dependencies including build tools for ProDy compilation
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RUN apt-get update -y && \
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apt-get install -y --no-install-recommends \
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wget \
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git \
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curl \
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ca-certificates \
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python3.11 \
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python3.11-venv \
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python3.11-dev \
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python3-pip \
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procps \
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build-essential \
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&& rm -rf /var/lib/apt/lists/* \
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&& update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.11 1 \
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&& update-alternatives --install /usr/bin/python python /usr/bin/python3.11 1
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# Upgrade pip
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RUN python3 -m pip install --no-cache-dir --upgrade pip setuptools wheel
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# Clone LigandMPNN repository
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RUN git clone https://github.com/dauparas/LigandMPNN.git /app/LigandMPNN
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# Set working directory to LigandMPNN
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WORKDIR /app/LigandMPNN
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# Install Python dependencies
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RUN pip3 install --no-cache-dir \
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biopython==1.79 \
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filelock==3.13.1 \
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fsspec==2024.3.1 \
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Jinja2==3.1.3 \
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MarkupSafe==2.1.5 \
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mpmath==1.3.0 \
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networkx==3.2.1 \
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numpy==1.23.5 \
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ProDy==2.4.1 \
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pyparsing==3.1.1 \
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scipy==1.12.0 \
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sympy==1.12 \
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typing_extensions==4.10.0 \
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ml-collections==0.1.1 \
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dm-tree==0.1.8
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# Install PyTorch with CUDA support
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RUN pip3 install --no-cache-dir \
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torch==2.2.1 \
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--index-url https://download.pytorch.org/whl/cu121
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# Download model parameters
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RUN mkdir -p /app/LigandMPNN/model_params && \
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wget -q https://files.ipd.uw.edu/pub/ligandmpnn/proteinmpnn_v_48_002.pt -O /app/LigandMPNN/model_params/proteinmpnn_v_48_002.pt && \
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wget -q https://files.ipd.uw.edu/pub/ligandmpnn/proteinmpnn_v_48_010.pt -O /app/LigandMPNN/model_params/proteinmpnn_v_48_010.pt && \
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wget -q https://files.ipd.uw.edu/pub/ligandmpnn/proteinmpnn_v_48_020.pt -O /app/LigandMPNN/model_params/proteinmpnn_v_48_020.pt && \
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wget -q https://files.ipd.uw.edu/pub/ligandmpnn/proteinmpnn_v_48_030.pt -O /app/LigandMPNN/model_params/proteinmpnn_v_48_030.pt && \
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wget -q https://files.ipd.uw.edu/pub/ligandmpnn/ligandmpnn_v_32_005_25.pt -O /app/LigandMPNN/model_params/ligandmpnn_v_32_005_25.pt && \
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wget -q https://files.ipd.uw.edu/pub/ligandmpnn/ligandmpnn_v_32_010_25.pt -O /app/LigandMPNN/model_params/ligandmpnn_v_32_010_25.pt && \
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wget -q https://files.ipd.uw.edu/pub/ligandmpnn/ligandmpnn_v_32_020_25.pt -O /app/LigandMPNN/model_params/ligandmpnn_v_32_020_25.pt && \
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wget -q https://files.ipd.uw.edu/pub/ligandmpnn/ligandmpnn_v_32_030_25.pt -O /app/LigandMPNN/model_params/ligandmpnn_v_32_030_25.pt && \
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wget -q https://files.ipd.uw.edu/pub/ligandmpnn/solublempnn_v_48_002.pt -O /app/LigandMPNN/model_params/solublempnn_v_48_002.pt && \
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wget -q https://files.ipd.uw.edu/pub/ligandmpnn/solublempnn_v_48_010.pt -O /app/LigandMPNN/model_params/solublempnn_v_48_010.pt && \
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wget -q https://files.ipd.uw.edu/pub/ligandmpnn/solublempnn_v_48_020.pt -O /app/LigandMPNN/model_params/solublempnn_v_48_020.pt && \
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wget -q https://files.ipd.uw.edu/pub/ligandmpnn/solublempnn_v_48_030.pt -O /app/LigandMPNN/model_params/solublempnn_v_48_030.pt && \
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wget -q https://files.ipd.uw.edu/pub/ligandmpnn/per_residue_label_membrane_mpnn_v_48_020.pt -O /app/LigandMPNN/model_params/per_residue_label_membrane_mpnn_v_48_020.pt && \
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wget -q https://files.ipd.uw.edu/pub/ligandmpnn/global_label_membrane_mpnn_v_48_020.pt -O /app/LigandMPNN/model_params/global_label_membrane_mpnn_v_48_020.pt && \
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wget -q https://files.ipd.uw.edu/pub/ligandmpnn/ligandmpnn_sc_v_32_002_16.pt -O /app/LigandMPNN/model_params/ligandmpnn_sc_v_32_002_16.pt && \
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ls -la /app/LigandMPNN/model_params/
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# Create wrapper script for ligandmpnn (using absolute path)
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RUN printf '#!/bin/bash\npython /app/LigandMPNN/run.py "$@"\n' > /usr/local/bin/ligandmpnn && \
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chmod +x /usr/local/bin/ligandmpnn
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# Create wrapper script for scoring (using absolute path)
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RUN printf '#!/bin/bash\npython /app/LigandMPNN/score.py "$@"\n' > /usr/local/bin/ligandmpnn-score && \
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chmod +x /usr/local/bin/ligandmpnn-score
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# Create input/output directories
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RUN mkdir -p /app/inputs /app/outputs
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# Set environment variables for model paths
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ENV LIGANDMPNN_MODEL_DIR=/app/LigandMPNN/model_params
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ENV PYTHONPATH=/app/LigandMPNN:${PYTHONPATH:-}
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WORKDIR /app/LigandMPNN
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CMD ["python", "run.py", "--help"]
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