BWA MCP Server

Bootstrap: docker
From: biocontainers/bwa:0.7.17--h7132678_9

%post
    # Install Python 3.11 and dependencies
    apt-get update && apt-get install -y \
        python3.11 \
        python3.11-venv \
        python3.11-dev \
        python3-pip \
        git \
        build-essential \
        && rm -rf /var/lib/apt/lists/*

    # Create virtual environment
    python3.11 -m venv /opt/venv
    . /opt/venv/bin/activate

    # Install Python dependencies
    pip install --no-cache-dir \
        mcp>=1.1.0 \
        pydantic>=2.0.0 \
        pydantic-settings>=2.0.0

    # Create directories
    mkdir -p /app/src
    mkdir -p /tmp/mcp-work
    chmod 755 /tmp/mcp-work

%files
    src /app/src
    pyproject.toml /app/

%environment
    export PATH="/opt/venv/bin:$PATH"
    export PYTHONPATH="/app"
    export BIO_MCP_TEMP_DIR="/tmp/mcp-work"
    export BIO_MCP_BWA_PATH="/usr/local/bin/bwa"

%runscript
    cd /app
    exec python -m src.server "$@"

%test
    # Verify BWA is available
    bwa
    
    # Test Python imports
    python -c "import src.server; print('BWA MCP server is ready')"

%help
    This container runs the Bio-MCP BWA server.
    
    Usage:
        singularity run bwa.sif
        
    Environment variables:
        BIO_MCP_TEMP_DIR: Temporary directory for processing (default: /tmp/mcp-work)
        BIO_MCP_BWA_PATH: Path to bwa binary (default: /usr/local/bin/bwa)
        BIO_MCP_TIMEOUT: Command timeout in seconds
        BIO_MCP_MAX_FILE_SIZE: Maximum input file size in bytes

%labels
    Author Bio-MCP Project
    Version 0.1.0
    Description MCP server for BWA sequence alignment