FROM python:3.10

# Install bedtools system dependency (required by pybedtools)
USER root
RUN apt-get update && apt-get install -y bedtools && rm -rf /var/lib/apt/lists/*

RUN useradd -m -u 1000 user && python -m pip install --upgrade pip
USER user
ENV PATH="/home/user/.local/bin:$PATH"

WORKDIR /app

COPY --chown=user ./requirements.txt requirements.txt
RUN pip install --no-cache-dir --upgrade -r requirements.txt

COPY --chown=user . /app
ENV MCP_TRANSPORT=http
ENV MCP_PORT=7860

EXPOSE 7860

CMD ["python", "pybedtools/mcp_output/start_mcp.py"]