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Using AlphaGenome with Docker

This guide explains how to use AlphaGenome with BioMCP in Docker containers.

Docker Setup

The BioMCP Docker image now includes AlphaGenome pre-installed. Here's how to use it:

1. Build the Docker Image

docker build -t biomcp-alphagenome .

2. Run with Docker Compose

Create or update your docker-compose.yml:

services:
  biomcp-server:
    build: .
    image: biomcp-alphagenome:latest
    container_name: biomcp-server
    ports:
      - "8000:8000"
    environment:
      - MCP_MODE=worker # Can be 'stdio' or 'worker'
      - ALPHAGENOME_API_KEY=${ALPHAGENOME_API_KEY}
    restart: unless-stopped

3. Set Your API Key

Create a .env file in the same directory as your docker-compose.yml:

ALPHAGENOME_API_KEY=your-api-key-here

Or set it in your shell:

export ALPHAGENOME_API_KEY='your-api-key-here'

4. Start the Container

docker-compose up -d

Usage in Container

Via Docker Exec

You can run AlphaGenome predictions directly in the container:

# Basic prediction
docker exec biomcp-server biomcp variant predict chr7 140753336 A T

# With tissue specificity
docker exec biomcp-server biomcp variant predict chr7 140753336 A T --tissue UBERON:0000310

Via MCP Worker Mode

When running in worker mode, the container exposes port 8000 for MCP connections. Configure your MCP client to connect to:

http://localhost:8000

Dockerfile Details

The Dockerfile includes these AlphaGenome-specific changes:

  1. Git Installation: Required to clone AlphaGenome repository
RUN apt-get update && apt-get install -y git
  1. AlphaGenome Installation: Cloned and installed during build
RUN git clone https://github.com/google-deepmind/alphagenome.git /tmp/alphagenome && \
    pip install /tmp/alphagenome && \
    rm -rf /tmp/alphagenome
  1. Environment Variable: API key passed through docker-compose 
    environment:
  - ALPHAGENOME_API_KEY=${ALPHAGENOME_API_KEY}

Troubleshooting

Container Can't Find API Key

Check that the environment variable is set:

docker exec biomcp-server env | grep ALPHAGENOME

AlphaGenome Import Errors

Verify AlphaGenome is installed in the container:

docker exec biomcp-server pip list | grep alphagenome

Rebuilding After Changes

If you update the Dockerfile or dependencies:

docker-compose build --no-cache
docker-compose up -d

Security Considerations

  1. API Key Security: Never commit your API key to version control
  2. Use .env Files: Keep API keys in .env files (add to .gitignore)
  3. Network Security: In production, use proper network isolation
  4. Volume Mounts: Be careful with volume mounts that might expose sensitive data

Example Docker Run Command

For standalone container without docker-compose:

docker run -d \
  --name biomcp-alphagenome \
  -p 8000:8000 \
  -e MCP_MODE=worker \
  -e ALPHAGENOME_API_KEY="$ALPHAGENOME_API_KEY" \
  biomcp-alphagenome:latest

Performance Notes

  • AlphaGenome predictions require network calls to Google's API
  • Container startup is slightly slower due to AlphaGenome installation
  • Consider using volume mounts for caching if making many predictions
  • The 1Mb genomic window option uses more memory and takes longer

Next Steps