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Quick Start

After completing installation, use these commands to get started.

srSILO Pipeline

Run Pipeline

# Update all enabled viruses (production)
ansible-playbook playbooks/srsilo/update-all-viruses.yml -i inventory.ini --become --ask-become-pass

# Or update a single virus
ansible-playbook playbooks/srsilo/update-pipeline.yml -i inventory.ini -e "srsilo_virus=rsva"

# Test with reduced resources (8GB RAM)
ansible-playbook playbooks/srsilo/update-all-viruses.yml -i inventory.ini \
  -e "@playbooks/srsilo/vars/test_vars.yml"

Setup Automation

# Setup daily automated runs at 2 AM
ansible-playbook playbooks/srsilo/setup-timer.yml -i inventory.ini

Check API Status

curl http://localhost:8083/sample/info  # COVID
curl http://localhost:8084/sample/info  # RSV-A

API Swagger UI:

  • COVID: http://localhost:8083/swagger-ui/index.html
  • RSV-A: http://localhost:8084/swagger-ui/index.html

Loculus

# Deploy W-ASAP Loculus to Kubernetes
ansible-playbook playbooks/loculus/deploy-loculus.yml -i inventory.ini

Monitoring Stack

# Deploy Prometheus + Grafana
ansible-playbook playbooks/monitoring/full.yml -i inventory.ini --ask-become-pass

Nginx Reverse Proxy

# Deploy Nginx with SSL termination
ansible-playbook playbooks/setup_nginx.yml -i inventory.ini --ask-become-pass

Next Steps