Docker Deployment

The BioNodulo core engine and editor are open source (GPL-3) and can be self-hosted. This is ideal for labs and institutions that want to run on their own infrastructure, behind their own firewall, or on HPC clusters.

Self-hosting gives you the editor and execution engine. Managed features — credit billing, team workspaces, AI paper analysis, and elastic scale-to-zero compute — are part of the cloud platform.

Quickstart with Docker Compose

# docker-compose.yml
services:
  bionodulo:
    image: ghcr.io/bionodulo/bionodulo:latest
    ports:
      - "8080:8080"
    environment:
      BIONODULO_SECRET_KEY: "change-me"
      BIONODULO_DATA_DIR: "/data"
    volumes:
      - bionodulo-data:/data
      # mount the host Docker socket so the engine can run containerized nodes
      - /var/run/docker.sock:/var/run/docker.sock
 
volumes:
  bionodulo-data:

docker compose up -d
# Open http://localhost:8080

Requirements

• A container runtime (Docker / containerd) on the host.
• Enough RAM for the heaviest node you intend to run (alignment/assembly are memory-bound).
• Persistent storage for the data volume (workflows, caches, outputs).

Running nodes

The engine launches containerized nodes via the host runtime, which is why the Docker socket is mounted. For HPC environments, the engine can instead submit jobs to a scheduler — see Configuration.

Updating

docker compose pull
docker compose up -d

Next

• Configuration
• Troubleshooting