FROM nvidia/cuda:12.2.0-runtime-ubuntu22.04

# Set non-interactive installation
ENV DEBIAN_FRONTEND=noninteractive

# Install system dependencies
RUN apt-get update && apt-get install -y \
    wget \
    git \
    python3 \
    python3-pip \
    build-essential \
    curl \
    python3-tk \
    && rm -rf /var/lib/apt/lists/*

# Set working directory
WORKDIR /opt/bioemu

# Install Python dependencies
RUN python3 -m pip install --upgrade pip

# Install BioEmu from PyPI
RUN pip install bioemu

# Install dependencies for free energy calculation
RUN pip install mdtraj scikit-learn pandas matplotlib seaborn

# Create directory for ColabFold and set environment variable
ENV COLABFOLD_DIR=/opt/colabfold

# Create cache directories with proper permissions
RUN mkdir -p ${COLABFOLD_DIR}/embeds_cache /tmp/colabfold_temp && \
    chmod -R 777 ${COLABFOLD_DIR} /tmp/colabfold_temp

# Pre-setup ColabFold during build to avoid runtime issues
RUN wget "https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/5fc8775114b637b5672234179c50e694ab057db4/install_colabbatch_linux.sh" -O ${COLABFOLD_DIR}/install_colabbatch_linux.sh && \
    chmod +x ${COLABFOLD_DIR}/install_colabbatch_linux.sh && \
    bash ${COLABFOLD_DIR}/install_colabbatch_linux.sh

# Create directories for input/output with proper permissions
RUN mkdir -p /data /results && chmod -R 777 /data /results

RUN mkdir -p /opt/bioemu/scripts/
COPY calculate_gibbs.py /opt/bioemu/scripts/
RUN chmod +x /opt/bioemu/scripts/calculate_gibbs.py

CMD ["/bin/bash"]