Dockerfile.server

# Production Dockerfile for Bio-Engine Server
FROM mirror.gcr.io/library/python:3.10-bullseye

# Build-time proxy ARGs
ARG HTTP_PROXY
ARG HTTPS_PROXY
ARG NO_PROXY
ARG http_proxy=$HTTP_PROXY
ARG https_proxy=$HTTPS_PROXY
ARG no_proxy=$NO_PROXY

# Copy custom CA certificates if any are provided (e.g. for HTTPS inspection proxy)
COPY certs/ /usr/local/share/ca-certificates/
RUN apt-get update && apt-get install -y ca-certificates && update-ca-certificates

# Tell python tools (pip, requests) to use the system CA certificate bundle
ENV PIP_CERT=/etc/ssl/certs/ca-certificates.crt
ENV REQUESTS_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt

# Install bioinformatics tools and system dependencies
RUN apt-get update && apt-get install -y \
    samtools \
    tabix \
    curl \
    procps \
    gcc \
    libpq-dev \
    python3-dev \
    && rm -rf /var/lib/apt/lists/*

# Download and install Tracy (bio-informatics tool)
RUN ARCH=$(uname -m) && \
    if [ "$ARCH" = "x86_64" ]; then TRACY_ARCH="amd64"; else TRACY_ARCH="arm64"; fi && \
    curl -L "https://github.com/gear-genomics/tracy/releases/download/v0.8.9/tracy-v0.8.9-linux-${TRACY_ARCH}" -o /usr/local/bin/tracy \
    && chmod +x /usr/local/bin/tracy

WORKDIR /app

# Copy requirements and install
COPY requirements.txt .
RUN pip install --no-cache-dir -r requirements.txt && \
    pip install --no-cache-dir python-multipart open-cravat

# Copy the rest of the application
COPY . .

# Create directory for persistent data
RUN mkdir -p /app/data

# Environment variables for the sidecar paths
ENV BIO_SAMTOOLS_PATH=samtools
ENV BIO_BGZIP_PATH=bgzip
ENV TRACY_PATH=tracy

EXPOSE 8000

# Run the FastAPI server
CMD ["python", "main.py", "--host", "0.0.0.0", "--port", "8000", "--data-dir", "/app/storage"]