biomodal duet software installation and running: Quick Start Guide

This quick start guide gives a concise overview of how to use our duet software installation and running guide: download, install and run the biomodal command line interface (CLI) for processing biomodal data.

Already installed?

If you’ve already installed the biomodal CLI and used it to run the duet pipeline, and now want help understanding the outputs of the pipeline, check out our Data Interpretation Guide.

Who Is This For?

This guide is for systems administrators and users who want to install and run the biomodal CLI tools.

• 🧑‍💻 Bioinformatician: You want to install the software for your own use on your workstation, compute cluster, or cloud environment.

• 🖥 Systems administrators: You want to install the software on a cluster for several users to run on their own data.

Overview: the duet Pipeline and CLI

The structure of the biomodal duet pipeline and biomodal CLI is shown in this diagram:

The typical user flow for the duet pipeline is as follows:

1. Download and install the biomodal CLI.

2. Define your instance location by setting the BIOMODAL_INSTANCE_DIRECTORY environment variable.

3. Run biomodal init to set up the necessary configuration files.

   • This will automatically download the latest version of the duet pipeline software.

4. Run biomodal run duet --test to make sure your system is properly configured.

   • Includes downloading a small test dataset and running the duet pipeline on it.

5. Run biomodal run duet with the proper settings to run the pipeline on your data.

   • Based on this example.

6. Read and interpret the results.

   • Further guidance on interpreting the outputs from the pipeline can be found in the data interpretation guide.

Forgotten Passwords

In the event of a lost or forgotten password, click here to reset it.

Other Capabilities

• You can download new versions of the duet pipeline software by running biomodal download.

• You can maintain multiple versions of the duet pipeline software on your system and choose to analyse with whichever you choose.

• The biomodal CLI also allows you perform other tasks, including:

  • Gathering relevant support information about your system with biomodal get diagnostics.

  • Generating support for a new reference genome with the reference genome pipeline.

How to use this guide

Navigation + searching

This guide is structured to help you quickly find the information you need. You can navigate through the major sections using the tabs at the top of this page, and then by using the table of contents on the right side of the page.

Additionally, you can use the search function in the top right-hand corner of the page to find specific topics or keywords across all biomodal software pages.

To get back to this page, click the ‘home’ icon.

Support links

For any questions or issues, please contact your biomodal support team at support@biomodal.com.

User documentation contents

• duet software installation and running guide
  • Getting started with the biomodal duet pipeline
  • Downloading the installation script
  • Installing the biomodal CLI
  • Using the CLI
  • Troubleshooting and optimisation
  • Updating the biomodal pipeline
  • Advanced analysis features
  • Target enrichment
  • Automation
  • Reference genome pipeline
  • Appendix

Release Notes

Links to release notes for pipeline and biomodal CLI versions are linked below.

Release version	Date
pipeline 1.5.0 / CLI 2.0.0	December 2025