52 lines
1.6 KiB
Docker
52 lines
1.6 KiB
Docker
FROM nvidia/cuda:12.2.0-runtime-ubuntu22.04
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# Set non-interactive installation
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ENV DEBIAN_FRONTEND=noninteractive
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# Install system dependencies
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RUN apt-get update && apt-get install -y \
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wget \
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git \
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python3 \
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python3-pip \
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build-essential \
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curl \
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python3-tk \
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&& rm -rf /var/lib/apt/lists/*
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# Set working directory
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WORKDIR /opt/bioemu
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# Install Python dependencies
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RUN python3 -m pip install --upgrade pip
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# Install BioEmu from PyPI
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RUN pip install bioemu
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# Install dependencies for free energy calculation
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RUN pip install mdtraj scikit-learn pandas matplotlib seaborn
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# Create directory for ColabFold and set environment variable
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ENV COLABFOLD_DIR=/opt/colabfold
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# Create cache directories with proper permissions
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RUN mkdir -p ${COLABFOLD_DIR}/embeds_cache /tmp/colabfold_temp && \
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chmod -R 777 ${COLABFOLD_DIR} /tmp/colabfold_temp
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# Pre-setup ColabFold during build to avoid runtime issues
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RUN wget "https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/5fc8775114b637b5672234179c50e694ab057db4/install_colabbatch_linux.sh" -O ${COLABFOLD_DIR}/install_colabbatch_linux.sh && \
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chmod +x ${COLABFOLD_DIR}/install_colabbatch_linux.sh && \
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bash ${COLABFOLD_DIR}/install_colabbatch_linux.sh
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# Create directories for input/output with proper permissions
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RUN mkdir -p /data /results && chmod -R 777 /data /results
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RUN mkdir -p /opt/bioemu/scripts/
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COPY calculate_gibbs.py /opt/bioemu/scripts/
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COPY calculate_binding.py /opt/bioemu/scripts/
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RUN chmod +x /opt/bioemu/scripts/calculate_gibbs.py
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RUN chmod +x /opt/bioemu/scripts/calculate_binding.py
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CMD ["/bin/bash"]
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