docker-compose.yml

version: "2"
name: scdatapipeline_project_${USER}    # Name of the project as appears when the container is running. Must be unique to each users

services:
  pipeline:
    image: scdatapipeline:latest
    container_name: scdatapipeline_instance_${USER}   # Name of the container as shown by docker container ls. 
    user: ${USERID}:${PROJECT_GID}   # The identity of the user inside the container. Files created on the host from the container will have this permissions
                                     # USERID can be found by running `id -u`	while the project ID can either be the user gid (id -g) or any other group the user belongs to
    group_add: 
      - 998     # Docker group ID on the host. It might not be 998 on your environment, use `getent group docker` to get the right id.
    environment:
      - SCDP_PATH_ROOT=/home/[PROJECT_NAME]    # Override the value of PATH_ROOT inside the container
    volumes:
      - /path/to/projects/[PROJECT_NAME]:/home/[PROJECT_NAME]                     # Mount the project's root under /home/[PROJECT_NAME] inside the container
      - /path/to/projects/singleCellAtlases:/path/to/projects/singleCellAtlases   # Example mount of external files, such as a folder containing the atlases. 
                                                                                  # For convenience, the path should be the same on the host and the container
      - /etc/passwd:/etc/passwd:ro                                                # The three following line allows for the user to be the same on the host and the container
      - /etc/group:/etc/group:ro
      - /etc/shadow:/etc/shadow:ro
    working_dir: /home/[PROJECT_NAME]   # Make the working directory of the container the project's root
    tty: true   # Required to access the container from tools such as Visual Studio Code's dev containers