Install Docker Desktop

Docker allows you to run software inside an isolated “container image” on your computer with all of that application’s needed dependencies. Make sure to install the version for your operating system.

• Mac-Intel
• Mac-AppleChip

MIRA Installation

• Open Docker Desktop, and once it is running:

Open Settings -> Features in development -> Experimental Features:

• Ensure “Access Experimental Features” and “Enable backround SBOM Indexing” are both checked on

Next, in Beta Features, enable “Use Rosetta for x86/amd66 emulation on Apple Silicon”. This will help MIRA run faster and remain more stable

Save these settings by clicking “Apply & restart”

Open the terminal, and copy/paste these commands

*NOTE: This MIRA_NGS folder was previously called FLU_SC2_SEQUENCING in documentation predating September 2024

mkdir ~/MIRA_NGS

cd ~/MIRA_NGS

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

docker compose up -d

If the docker compose command fails with a permissions error, please try again with sudo added before the command.

You are now running MIRA! You can proceed to Running MIRA with Oxford Nanopore data or Illumina data

If these instructions show errors, please refer to our Troubleshooting page or email us at idseqsupport@cdc.gov

Optional: Install a sequence viewer to open output .fastas

• Jalview

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 2b folders into MIRA_NGS so that the file structure looks like: /MIRA_NGS/tiny_test_run_flu/fastq_pass/barcode##s/ and /MIRA_NGS/tiny_test_run_sc2/fastq_pass/barcode##s/

Upon successful installation, you can proceed to running MIRA with Oxford Nanopore data or Illumina data