Bio-MCP BLAST

# Use biocontainers BLAST image FROM biocontainers/blast:2.15.0 AS blast-tools # Build MCP server layer FROM python:3.11-slim # Install system dependencies RUN apt-get update && apt-get install -y \ libgomp1 \ && rm -rf /var/lib/apt/lists/* # Copy BLAST binaries from biocontainer COPY --from=blast-tools /usr/local/bin/blastn /usr/local/bin/ COPY --from=blast-tools /usr/local/bin/blastp /usr/local/bin/ COPY --from=blast-tools /usr/local/bin/makeblastdb /usr/local/bin/ COPY --from=blast-tools /usr/local/bin/blastdbcmd /usr/local/bin/ # Install Python dependencies WORKDIR /app COPY pyproject.toml . RUN pip install -e . # Copy server code COPY src/ ./src/ # Create non-root user RUN useradd -m -u 1000 mcp && \ mkdir -p /tmp/mcp-blast && \ chown -R mcp:mcp /app /tmp/mcp-blast USER mcp # Set environment variables ENV BIO_MCP_TEMP_DIR=/tmp/mcp-blast ENV PATH="/usr/local/bin:${PATH}" # Health check HEALTHCHECK --interval=30s --timeout=3s --start-period=5s --retries=3 \ CMD python -c "import src.server" || exit 1 # Run the server CMD ["python", "-m", "src.server"]