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Source: vignettes/quick-start-ubuntu.Rmd
quick-start-ubuntu.Rmd

QUICK START STUFF: ## Quick Start on Ubuntu OS: Need to set up an Ubuntu OS? Follow instructions in Getting Started.

Install Docker CLI and Docker Compose: 

sudo apt-get update
sudo apt-get install ca-certificates curl gnupg lsb-release
  • During installation, you will be prompted to enter ‘y’ or ‘n’ to proceed. Each time, input ‘y’ and click Enter 
sudo mkdir -p /etc/apt/keyrings
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /etc/apt/keyrings/docker.gpg
echo "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable" | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
sudo apt-get update
sudo chmod a+r /etc/apt/keyrings/docker.gpg
sudo apt-get update
sudo apt-get install docker-ce docker-ce-cli containerd.io docker-compose-plugin
  1. Verify successful installation
sudo docker run hello-world
  • This command downloads a test image and runs it in a container. When the container runs, it prints a confirmation message and exits.

MIRA Container Installation with Docker Compose

  • Create a folder called MIRA_NGS to save your sequencing reads to. From the command line, run:
mkdir ~/MIRA_NGS

cd ~/MIRA_NGS
  • Download the install yml:
 curl https://raw.githubusercontent.com/CDCgov/MIRA/prod/docker-compose-cdcgov.yml | sed "s%/path/to/data%$(pwd)/%g" > docker-compose.yml
  • Run the install script:
sudo docker compose up -d

Test your MIRA Setup

  • Click here to download tiny test data from ONT Influenza genome and SARS-CoV-2-spike - 40Mb
  • Click here for the above data set + full genomes of Influenza and SARS-CoV-2 from Illumina MiSeqs - 1Gb
  • unzip the file and find two folders:
    1. tiny_test_run_flu
    2. tiny_test_run_sc2
  • move these folders into MIRA_NGS
    • if you cannot find the MIRA_NGS folder in your Linux section of file explorer, look in Linux–>home–>your username
  • Open your browser and type http://localhost:8020 in the address bar.
  • Click Refresh Run Listing in MIRA, you should now see these folders listed.
  • Click Download Samplesheet.
    • This will give you an excel sheet with available barcodes populated. Add in our samplenames for ONT data (Illumina data will self identify samplenames based on fastqs)
  • Save the samplesheet and then upload it by clicking on Drag and Drop your Samplesheet or Click and Select the File
  • In the dropdown box ‘What kind of data is this?’, select the correct data type.
    • If SC2 full genome, also select your primers.
  • Click ‘START GENOME ASSEMBLY’
  • Toggle ‘Watch IRMA progress’ to see IRMA’s stdout stream.
  • When “IRMA is finished!” is displayed, Click “DISPLAY IRMA RESULTS”