Opal/Armadillo Local Deployment

Dick Postma and Xavier Escribà Montagut

Overview

Goal: Deploy Armadillo locally using Docker Compose

Services & Roles

🏢 Armadillo (Molgenis DataSHIELD Server) - Main DataSHIELD server and admin UI

🔧 Rock (R Server) - Executes R/DataSHIELD calls from Armadillo

🗄️ Filesystem (File Store) - Files are stored locally on disk.

File Structure

local-deploy-armadillo
├── config
    ├── application.yml ( Main armadillo configuration )
├── data                ( Local storage )
├── docker-compose.yml
└── logs                ( Armadillo logfiles )

Step 1: Armadillo configuration

armadillo:
  docker-management-enabled: false
  docker-run-in-container: true
  profiles:
    - name: default
      image: datashield/rock-base:latest
      port: 8085
      host: rserver
      package-whitelist:
        - dsBase
      function-blacklist: [ ]
      options:
        datashield:
          seed: 342325352

# required settings:
spring:
  security:
    user:
      # please change this admin password!
      password: admin!!!

storage:
  ## to change location of the data storage
  root-dir: /data

Step 2: Docker Compose (simplified)

services:
 armadillo:
   image: molgenis/molgenis-armadillo:latest
   platform: linux/amd64
   ports:
     - "8000:8080"
   volumes:
     - ./logs:/app/logs
     - ./data:/data
     - /var/run/docker.sock:/var/run/docker.sock
     - ./config:/config
   networks:
     - armadillo-workshop

 rserver:
   image: datashield/rock-base:latest
   platform: linux/amd64

Step 3: Deploy the Stack

# Start all services
docker-compose up -d

# Check status
docker-compose ps

# Monitor Opal logs
docker-compose logs -f armadillo 

First start: May take a minute while images are pulled

Access: Open http://localhost:8000 in your browser

Login: User admin + password from config

Step 4: Test DataSHIELD Connection

library(dsBaseClient)
library(DSI)
library(DSMolgenisArmadillo)


url <- "http://localhost:8000"
builder <- DSI::newDSLoginBuilder()

builder$append(
  server = "armadillo",
  url = url,
  #token = token,
  user = "admin",
  password = "admin",
  driver = "ArmadilloDriver",
  profile = "default")

logindata <- builder$build()
conns <- DSI::datashield.login(logins = logindata)


ds.ls()

Note: SSL verification disabled for local testing only!

Key Configuration Points

Network Setup

• All services on armadillo-workshop Docker network
• Exposed ports: 8000: HTTP

Persistence

• Named volumes preserve data across restarts
• Remove volumes to reset completely

Troubleshooting

• Ensure port 8000 is free on your system.

Reset stack

docker compose down -v 
docker compose up --build

Summary

Operational Armadillo datashield Setup! Full stack setup (keycloak) available at github!