fmriprep-workbench/docker-compose.yml at main · shawntz/fmriprep-workbench · GitHub

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version: '3.8'

services:
  fmriprep-workbench:
    image: shawnschwartz/fmriprep-workbench:latest
    container_name: fmriprep-workbench
    hostname: fmriprep-workbench

    # Run as current user to maintain file permissions
    user: "${UID:-1000}:${GID:-1000}"

    # Keep container running
    command: sleep infinity

    # Interactive terminal
    stdin_open: true
    tty: true

    # Volume mounts
    volumes:
      # Workspace (current directory)
      - ./:/opt/fmriprep-workbench/workspace:rw

      # Configuration files
      - ./config.yaml:/data/config/config.yaml:ro
      - ./all-subjects.txt:/data/subjects/all-subjects.txt:ro

      # Logs directory
      - ./logs:/data/logs:rw

      # Cache directories (host home directory)
      - ${HOME}/.cache/templateflow:/data/cache/templateflow:rw
      - ${HOME}/.cache/fmriprep:/data/cache/fmriprep:rw

      # Optional: Mount study data directories
      # Uncomment and modify paths as needed
      # - /path/to/your/study:/data/study:rw
      # - /path/to/containers:/data/containers:ro

    # Environment variables
    environment:
      - WORKBENCH_WORKSPACE=/opt/fmriprep-workbench/workspace
      - WORKBENCH_VERSION=0.2.0
      - FSLDIR=/usr/share/fsl/5.0
      - FSLOUTPUTTYPE=NIFTI_GZ
      - PATH=/usr/share/fsl/5.0/bin:/opt/fmriprep-workbench:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

    # Resource limits (adjust as needed)
    deploy:
      resources:
        limits:
          cpus: '8'
          memory: 16G
        reservations:
          cpus: '2'
          memory: 4G

    # Restart policy
    restart: unless-stopped

    # Network mode
    network_mode: bridge

# Named volumes (optional, for persistent data)
volumes:
  templateflow_cache:
  fmriprep_cache:

# Networks (optional)
networks:
  default:
    name: fmriprep-workbench-network