How to upgrade MIRA to the lastest version

MIRA version 1 was installed with a data directory of FLU_SC2_SEQUENCING, versions 2.0.0+ are reccomended to be installed with MIRA_NGS as the data directory. If you are upgrading from v1.1.X, you may wish to retain your FLU_SC2_SEQUENCING folder as the MIRA data location.

Upgrading MIRA with four containers (version 1.1.4) to MIRA single container (version 2.0.0)

1. Open a terminal (Ubuntu if you installed WSL2 with this instructions, Terminal if you are using a Mac). cd to the folder with your sequence run data:

    cd ~/FLU_SC2_SEQUENCING

2. Remove current running MIRA containers:

    docker rm -f mira spyne irma dais

3. Remove older MIRA image versions (or iSpy or IRMA-spy if that’s what you had installed)

    sudo docker rmi -f $(docker images | grep -e irma -e dais -e mira -e spyne | tr -s " " | cut -f3 -d" ")

4. Download the installation script from the internet:

    curl https://raw.githubusercontent.com/CDCgov/MIRA/prod/docker-compose-cdcgov.yml | sed "s%/path/to/data%$(pwd)/%g" > docker-compose.yml

   if you get a permissions error here, first run sudo rm docker-compose.yml then try again

5. After you ensure that your Docker Desktop application is open, run the install script with sudo and docker compose:

    sudo docker compose up -d

Upgrading MIRA single container (version 2.0.0+)

1. Open a terminal (Ubuntu if you installed WSL2 with this instructions, Terminal if you are using a Mac). cd to the folder with your sequence run data:

    cd ~/MIRA_NGS

2. Remove current running MIRA container:

    docker rm -f mira

3. Remove older MIRA image version:

    sudo docker rmi -f $(docker images | grep -e mira | tr -s " " | cut -f3 -d" ")

4. Download the installation script from the internet:

    curl https://raw.githubusercontent.com/CDCgov/MIRA/prod/docker-compose-cdcgov.yml | sed "s%/path/to/data%$(pwd)/%g" > docker-compose.yml

   if you get a permissions error here, first run sudo rm docker-compose.yml then try again

5. After you ensure that your Docker Desktop application is open, run the install script with sudo and docker compose:

    sudo docker compose up -d