scout/Dockerfile-server at main · Clinical-Genomics/scout · GitHub

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###########
# BUILDER #
###########
FROM ghcr.io/astral-sh/uv:python3.14-bookworm AS python-builder

WORKDIR /app

# Copy the project files needed to configure dependencies build into the image
COPY --chmod=644 pyproject.toml uv.lock README.md ./

RUN uv venv --relocatable
RUN uv sync --frozen --no-install-project --no-editable
RUN uv pip install --no-cache-dir gunicorn

#########
# FINAL #
#########
FROM ghcr.io/astral-sh/uv:python3.14-bookworm-slim

LABEL about.home="https://github.com/Clinical-Genomics/scout"
LABEL about.documentation="https://clinical-genomics.github.io/scout"
LABEL about.tags="Clinical,Variant triage,WGS,WES,Rare diseases,VCF,variants,SNV,Massively parallel sequencing,Next generation sequencing"
LABEL about.license="MIT License (MIT)"

RUN apt-get update && \
    apt-get -y upgrade && \
    apt-get -y install --no-install-recommends git wkhtmltopdf && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/*

# Create a non-root user to run commands
RUN groupadd --gid 1000 worker && useradd -g worker --uid 1000 --shell /usr/sbin/nologin --create-home worker

ENV PATH="/home/worker/app/.venv/bin:$PATH"
WORKDIR /home/worker/app

# Copy current app code to app dir
COPY --chown=root:root --chmod=755 . /home/worker/app

# Copy virtual environment from builder
COPY --from=python-builder /app/.venv /home/worker/app/.venv

# Ensure worker owns everything in venv
RUN chown -R worker:worker /home/worker/app/.venv

# Switch to non-root user
USER worker

# Install Scout app
RUN uv pip install --no-cache-dir .[coverage]

ENV GUNICORN_WORKERS=1
ENV GUNICORN_THREADS=1
ENV GUNICORN_BIND="0.0.0.0:8000"
ENV GUNICORN_TIMEOUT=400
ENV GUNICORN_MAXREQUESTS=1200

CMD ["sh", "-c", "/home/worker/app/.venv/bin/gunicorn \
    --workers=$GUNICORN_WORKERS \
    --bind=$GUNICORN_BIND \
    --threads=$GUNICORN_THREADS \
    --timeout=$GUNICORN_TIMEOUT \
    --max-requests=$GUNICORN_MAXREQUESTS \
    --proxy-protocol \
    --forwarded-allow-ips=10.0.2.100,127.0.0.1 \
    --log-syslog \
    --access-logfile - \
    --error-logfile - \
    --log-level=debug \
    scout.server.auto:app"]