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

ENV DEBIAN_FRONTEND=noninteractive

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

WORKDIR /opt/bioemu

RUN python3 -m pip install --upgrade pip && \
    pip install --no-cache-dir bioemu mdtraj scikit-learn pandas matplotlib seaborn

# Add user entry for UID 1000 (k8s default) to avoid getpwuid errors
RUN useradd -u 1000 -m -s /bin/bash nextflow || true

RUN mkdir -p /opt/bioemu/scripts/ /data /results && chmod -R 777 /data /results

COPY calculate_gibbs.py /opt/bioemu/scripts/
COPY scripts/calculate_binding.py /opt/bioemu/scripts/

RUN chmod +x /opt/bioemu/scripts/calculate_gibbs.py /opt/bioemu/scripts/calculate_binding.py

CMD ["/bin/bash"]