Getting started

Getting started#

Prerequisites#

  • Docker — required for running pipelines. Install Docker Desktop for macOS or Linux.

GLACIER bundles its own Java Runtime Environment and Nextflow, so you do not need to install those separately.

Windows users: GLACIER uses WSL2 under the hood for Nextflow execution. Docker is bundled inside the WSL2 image — you do not need to install Docker Desktop separately. The Settings → Environment tab provides guided setup for installing and configuring WSL2.

Installation#

Download the latest GLACIER release for your platform from the GitHub Releases page.

Platform

Format

macOS (Intel)

.dmg

macOS (Apple Silicon)

.dmg

Windows

.exe installer

Linux

.AppImage or .deb

Open the downloaded file and follow the installer prompts. Once installed, launch GLACIER from your Applications folder, Start menu, or desktop shortcut.

Developers: If you want to build from source, see Building from source.

First launch#

When you start GLACIER for the first time you will see an empty Library page. Your first step is to add a catalogue.

  1. Click the Actions button in the top-left corner.

  2. Select Add a Catalogue.

  3. Enter artic-network/glacier-catalogue and click Add.

GLACIER will clone the catalogue repository and display its contents. You should see three sections: workshop, general, and MPXV, each containing workflow cards.

A shorthand name like artic-network works if the organisation has a repository called glacier-catalogue. When in doubt, use the full owner/repo format.

Quick start walkthrough#

  1. In the workshop section, find the amplicon-nf workflow card.

  2. Click Install to clone the workflow repository.

  3. Once installed, click the workflow card. The Parameters page opens.

  4. Review the parameters (they are populated from the workflow’s nextflow_schema.json), or accept the defaults.

  5. Select an execution profile (e.g. standard) from the dropdown.

  6. Click Launch to start the pipeline.

GLACIER will create a named instance (e.g. brave-lion) and navigate to the Monitor page where you can track progress, view logs, and inspect reports.

Building from source#

If you prefer to build the application yourself:

git clone https://github.com/ARTIC-Kraemer-Lab/GLACIER.git
cd GLACIER
npm install
npm start

You will need Node.js 18+ and npm installed. The first build may take a minute while TypeScript compiles the backend and Vite bundles the frontend.

Next steps#

  • Tutorial: running raccoon-nf — walk through a complete workflow lifecycle with raccoon-nf.

  • Catalogues — learn how to browse, organise, and maintain catalogues.

  • Workflows — detailed guide to installing, configuring, and launching workflows.

  • Monitoring runs — monitoring pipeline execution and inspecting outputs.

  • Settings — configuring GLACIER to suit your environment.

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