debug-igv-studio

name	debug-igv-studio
description	Troubleshoot IGV Studio issues in Seqera Platform. Use when studios fail to start, show errors, data not discovered, or browser console shows 404s.
compatibility	Requires tw CLI, TOWER_ACCESS_TOKEN, browser DevTools access.
metadata	{"author":"Seqera/edmundmiller","version":"1.0"}

Debug IGV Studio

Troubleshoot IGV Studio issues in Seqera Platform.

Quick Diagnosis Checklist

1. Browser Console - Check for 404s, JS errors (F12 → Console)
2. Studio Status - Is it running? tw studios list -w scidev/testing
3. Container Logs - Check Seqera Platform UI logs
4. Data Discovery - Did Fusion mount data in time?

Common Issues

404 Not Found on JavaScript/CSS files

Symptom: Browser console errors like:

GET /node_modules/igv/dist/igv.esm.js 404
GET /resources/...js 404

Cause: Web app source code copied but never built.

Fix: Ensure Dockerfile uses multi-stage build. See references/DOCKERFILE-FIX.md.

CORS Errors

Symptom: Cross-Origin Request Blocked when loading remote files.

Cause: Data server doesn't allow cross-origin requests.

Fix: Configure CORS on data server or use Fusion data links (nginx serves with CORS enabled).

Files Not Auto-Discovered

Check inside container:

ls -la /workspace/data/           # Fusion mount
cat /tmp/discovered-tracks.json   # Discovery output
DEBUG=1 /usr/local/bin/discover-data-links.sh  # Re-run with debug

Studio Stuck in "Starting"

Causes:

• Container crash (check logs)
• Loop device permission (must run as root)
• Image pull failure (check compute env credentials)

could not open loop device: permission denied

Container not running as root. Remove any USER directive from Dockerfile.

Debugging Workflow

# 1. Check existing studios
tw studios list -w scidev/testing

# 2. View studio details
tw studios view --name "IGV Studio" -w scidev/testing

# 3. Check logs in Seqera Platform UI

# 4. Stop broken studio
tw studios stop --session-id <SESSION_ID> -w scidev/testing

# 5. Fix and rebuild
IMAGE_URL=$(wave -f Dockerfile --context . --platform linux/amd64 --await --tower-token "$TOWER_ACCESS_TOKEN")

# 6. Launch new studio
tw studios add --name "IGV Studio" -w scidev/testing --custom-template "$IMAGE_URL" --compute-env "seqera_aws_london_fusion_nvme" --auto-start

See references/DATA-DISCOVERY.md for data discovery details. See references/DOCKERFILE-FIX.md for build fixes.