Created a dedicated Dockerfile for running a prod server

Dockerfile

@@ -9,7 +9,7 @@ WORKDIR /app
 
 # Install Scout dependencies
 COPY requirements.txt .
-RUN pip install --no-cache-dir -r requirements.txt gunicorn
+RUN pip install --no-cache-dir -r requirements.txt
 
 
 #########
@@ -35,7 +35,7 @@ ENV PATH="/venv/bin:$PATH"
 RUN echo export PATH="/venv/bin:\$PATH" > /etc/profile.d/venv.sh
 
 # Create a non-root user to run commands
-RUN groupadd --gid 10001 worker && useradd -g worker --uid 10001 --shell /usr/sbin/nologin --create-home worker
+RUN groupadd --gid 1000 worker && useradd -g worker --uid 1000 --shell /usr/sbin/nologin --create-home worker
 
 # Copy virtual environment from builder
 COPY --chown=worker:worker --from=python-builder /venv /venv

Dockerfile-server

@@ -0,0 +1,67 @@
+###########
+# BUILDER #
+###########
+FROM clinicalgenomics/python3.8-cyvcf2-venv:1.0 AS python-builder
+
+ENV PATH="/venv/bin:$PATH"
+
+WORKDIR /app
+
+# Install Scout dependencies
+COPY requirements.txt .
+RUN pip install --no-cache-dir -r requirements.txt gunicorn
+
+#########
+# FINAL #
+#########
+FROM python:3.8-slim
+
+LABEL about.home="https://github.com/Clinical-Genomics/scout"
+LABEL about.documentation="https://clinical-genomics.github.io/scout"
+LABEL about.tags="WGS,WES,Rare diseases,VCF,variants,SNP,Next generation sequencing"
+LABEL about.license="MIT License (MIT)"
+
+# Install base dependencies
+RUN apt-get update && \
+     apt-get -y upgrade && \
+     apt-get -y install -y --no-install-recommends libpango-1.0-0 libpangocairo-1.0-0 && \
+     apt-get clean && \
+     rm -rf /var/lib/apt/lists/*
+
+# Do not upgrade to the latest pip version to ensure more reproducible builds
+ENV PIP_DISABLE_PIP_VERSION_CHECK=1
+ENV PATH="/venv/bin:$PATH"
+RUN echo export PATH="/venv/bin:\$PATH" > /etc/profile.d/venv.sh
+
+# 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
+
+# Copy virtual environment from builder
+COPY --chown=worker:worker --from=python-builder /venv /venv
+
+WORKDIR /home/worker/app
+COPY . /home/worker/app
+
+# Install only Scout app
+RUN pip install --no-cache-dir --editable .[coverage]
+
+# Run the app as non-root user
+USER worker
+
+ENV GUNICORN_WORKERS=1
+ENV GUNICORN_THREADS=1
+ENV GUNICORN_BIND="0.0.0.0:8000"
+ENV GUNICORN_TIMEOUT=400
+
+CMD gunicorn \
+    --workers=$GUNICORN_WORKERS \
+    --bind=$GUNICORN_BIND  \
+    --threads=$GUNICORN_THREADS \
+    --timeout=$GUNICORN_TIMEOUT \
+    --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