Frequently asked questions

How do I get help?

Great question!!

MIRA is under active development. If you need help, would like to contribute, or simply want to talk about the project with like-minded individuals, we have a number of open channels for communication.

• Send us an email at idseqsupport@cdc.gov

• To report bugs or file feature requests, use the issue tracker on Github.

• To contribute code submit a pull request on Github.

How to remove containers. This is a good idea if you are having trouble with your version and need a fresh start. This will not have any effect on your sequencing data.

iSpy uninstall

docker stop ispy
docker rm ispy
docker rmi ispy

IRMA-SPY uninstall

docker stop irma-spy
docker rm irma-spy
docker rmi irma-spy

MIRA uninstall

1. Open an Ubuntu terminal

2.  # Show running containers
    docker ps
   
    # Stop running container you want to update. In this example we are updating mira and spyne.
    docker stop mira spyne irma dais
   
    # Delete containers
    docker rm mira spyne irma dais
   
    # Delete images
    docker rmi mira spyne irma dais

3. Install the new MIRA and spyne containers: See Docker Desktop MIRA installation

How do I customize the number of cores MIRA uses?

This is best achieved by setting resources in the docker-compose.yml for a container’s deploy settings:

For example:

spyne: 
    container_name: spyne
    image: spyne
    build: 
      context: *spyne-git-version 
    depends_on:
      - dais
      - irma
    restart: always
    networks:
      - backend
    volumes:
      - *data-volume
      - *docker-socket
    command: tail -f /dev/null
    deploy:
      resources:
        limits:
          cpus: '0.50'
          memory: 50M
        reservations:
          cpus: '0.25'
          memory: 20M

Read more here in the official Docker Docs

Docker compose operations

Command	Description
docker compose build	Build or rebuild services
docker compose config	Parse, resolve and render compose file in canonical format
docker compose cp	Copy files/folders between a service container and the local filesystem
docker compose create	Creates containers for a service.
docker compose down	Stop and remove containers, networks
docker compose events	Receive real time events from containers.
docker compose exec	Execute a command in a running container.
docker compose images	List images used by the created containers
docker compose kill	Force stop service containers.
docker compose logs	View output from containers
docker compose ls	List running compose projects
docker compose pause	Pause services
docker compose port	Print the public port for a port binding.
docker compose ps	List containers
docker compose pull	Pull service images
docker compose push	Push service images
docker compose restart	Restart service containers
docker compose rm	Removes stopped service containers
docker compose run	Run a one-off command on a service.
docker compose start	Start services
docker compose stop	Stop services
docker compose top	Display the running processes
docker compose unpause	Unpause services
docker compose up	Create and start containers
docker compose version	Show the Docker Compose version information