Installation

Compatibility

Nomadic runs on macOS or Linux. Windows is currently not supported.

Requirements

To install Nomadic, you will need to install the package manager conda or mamba. Mamba is faster and is recommended.

To install Mamba, run:

curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"

or

wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"

Then run the script with:

bash Miniforge3-$(uname)-$(uname -m).sh

Steps

Open a terminal window and type:

conda create -c bioconda -n nomadic nomadic

Or, if you are using Mamba:

mambda create -c bioconda -n nomadic nomadic

Nomadic should now be installed in it's own conda environment.

Test installation

To test the installation, we will enter the conda environment:

conda activate nomadic

Then type:

nomadic --help

If nomadic has been installed successfully, you should see a set of available commands:

Usage: nomadic [OPTIONS] COMMAND [ARGS]...

  Mobile sequencing and analysis in real-time

Options:
  --version  Show the version and exit.
  --help     Show this message and exit.

Commands:
  start      Start a workspace.
  download   Download reference genomes.
  realtime   Run analysis in real-time.
  dashboard  Just run the dashboard.