FAQ / Troubleshooting

FAQ / Troubleshooting#

General#

Where are my workflows and data stored?#

  • Config directory: catalogues, cloned workflow repositories, and the instances database.

  • Documents directory: instance run directories (parameters, logs, work directories, reports).

You can view and change these paths in Settings → General.

Can I use GLACIER without Docker?#

No — Docker is required to run Nextflow pipelines. GLACIER checks for Docker on startup and shows a warning in the Library page if it is not found.

  • macOS / Linux: Install Docker Desktop and ensure the daemon is running.

  • Windows: Docker is bundled inside the WSL2 image. Follow the guided setup in Settings → Environment to configure WSL2.

Can I use GLACIER for workflows that are not from the ARTIC Network?#

Yes. You can add any GitHub repository that contains a valid Nextflow workflow (with a nextflow_schema.json file). Use Actions → Add Repository to add your own workflows.

Catalogue issues#

I typed artic-network but nothing happened#

The shorthand name works only if the organisation has a repository called glacier-catalogue. Try adding the catalogue using the full owner/repo form: artic-network/glacier-catalogue.

Adding a catalogue from GitHub requires internet access. If you are behind a corporate proxy, you may need to configure Git proxy settings.

If you do not have internet access, you can use shards — portable bundles that contain workflows, containers, and data — to load catalogues and workflows offline.

Some workflows have broken URLs in the catalogue#

The ARTIC Network catalogue intentionally includes some entries with invalid repository URLs (e.g. artic-network/raccoon_nf — note the underscore). These are used for testing error handling. Workflows with valid URLs will install normally.

Workflow issues#

My workflow is stuck at “created”#

The instance was created but never launched. Open the Instances page, click the status icon to open the Parameters page, and click Launch.

My workflow failed — where do I look for errors?#

  1. Monitor → Logs tab — check stderr and nextflow.log for error messages.

  2. Monitor → Progress tab — look for process nodes with red error icons.

  3. Click the ⋮ menu on a failed process and inspect .command.err and .command.out for task-level errors.

How do I update an installed workflow?#

On the workflow card in the Library, click the ⋮ menu and select Check for updates. If a newer commit is available on the default branch, GLACIER will pull the latest changes.

Performance#

Why is the progress tree not updating?#

The Progress tab refreshes every 5 seconds. If your workflow is very short, it may complete before the first refresh. Check the Logs tab for the final output.

The Monitor page feels slow#

The Logs tab refreshes every 1 second. For workflows with high-output processes, this can be demanding. Switch to the Progress or Reports tab if you do not need live log streaming.

Environment#

Windows: WSL2 setup fails#

Open Settings → Environment and use the guided WSL2 setup buttons:

  1. Install WSL2 — enables the Windows feature.

  2. Configure WSL2 — downloads Ubuntu 22.04 and installs Java, Docker, Nextflow.

If this fails, ensure Windows is up to date and virtualization is enabled in your BIOS.

macOS: “Docker not found”#

Install Docker Desktop for Mac and ensure it is running (the whale icon should appear in your menu bar).

Web deployment#

Warning

Web server mode is experimental and not fully supported. Some features may behave differently or be unavailable compared to the desktop application.

The web server won’t start#

Make sure you have run npm run build first — the server depends on compiled output in dist/.

Can I run the web server behind a reverse proxy?#

Yes. The server listens on port 3030 by default. Configure nginx, Caddy, or another reverse proxy to forward requests to http://localhost:3030.

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