Configuration Reference¶

srSILO Configuration¶

Enable Viruses¶

In roles/srsilo/defaults/main.yml:

srsilo_enabled_viruses:
  - covid
  - rsva

Per-Virus Configuration¶

In group_vars/srsilo/main.yml:

srsilo_virus_config:
  covid:
    fetch_days: 90           # Days of data to fetch
    fetch_max_reads: 172500000  # Max reads to fetch
    chunk_size: 1000000      # Chunk size for processing
    docker_memory_limit: 340g  # Memory limit for SILO container
  rsva:
    fetch_days: 90
    fetch_max_reads: 50000000
    chunk_size: 500000
    docker_memory_limit: 340g

Global Settings¶

srsilo_retention_days: 3        # Delete indexes older than N days
srsilo_retention_min_keep: 2    # Always keep at least M indexes

Virus Registry¶

In roles/srsilo/defaults/main.yml:

srsilo_viruses:
  covid:
    organism: covid
    instance_name: wise-sarsCoV2
    lapis_port: 8083
    silo_port: 8081
  rsva:
    organism: rsva
    instance_name: wise-rsva
    lapis_port: 8084
    silo_port: 8082

Loculus Configuration¶

Required Variables¶

Set in host_vars/ or group_vars/:

Variable	Description
`kubectl_context`	kubectl context name
`helm_chart_path`	Path to Loculus Helm chart

Application Settings¶

In group_vars/loculus/main.yml:

Application name, host, organisms
URL configurations
Feature flags

Secrets¶

In group_vars/loculus/vault.yml (encrypted):

Database credentials
Keycloak settings
S3 credentials
Service account passwords

Defaults¶

In roles/loculus/defaults/main.yml:

Variable	Default	Description
`loculus_temp_dir`	`/tmp/loculus`	Temp directory for deployment
`loculus_cleanup_temp_files`	`true`	Clean up temp files after deployment
`loculus_kubeconfig_path`	`~/.kube/config`	Path to kubeconfig

Monitoring Configuration¶

LAPIS Instances¶

In group_vars/monitoring/main.yml:

lapis_instances:
  - name: covid
    url: https://lapis.wasap.genspectrum.org
  - name: rsva
    url: https://lapis.wasap.genspectrum.org/rsva

Metrics to Collect¶

lapis_metrics:
  - name: info_count
    path: $.info.count
  - name: response_time
    path: $.responseTime

Grafana¶

Variable	Description
`grafana_admin_password`	Admin password (use vault)

Nginx Configuration¶

Domain Settings¶

In roles/nginx/defaults/main.yml:

Variable	Default	Description
`nginx_domain_name`	`wasap.genspectrum.org`	Base domain name

Port Mappings¶

Variable	Default	Description
`nginx_lapis_covid_port`	`8083`	COVID LAPIS port
`nginx_lapis_rsva_port`	`8084`	RSVA LAPIS port
`nginx_silo_covid_port`	`8081`	COVID SILO port
`nginx_silo_rsva_port`	`8082`	RSVA SILO port

SSL Certificates¶

Variable	Description
`nginx_ssl_certificate_path`	Main domain SSL cert
`nginx_ssl_certificate_key_path`	Main domain SSL key
`nginx_lapis_ssl_certificate_path`	LAPIS subdomain SSL cert
`nginx_silo_ssl_certificate_path`	SILO subdomain SSL cert
`nginx_loculus_ssl_certificate_path`	Loculus subdomain SSL cert

Sites¶

nginx_sites:
  - name: wasap-scout
    template: wasap-scout.j2
  - name: lapis
    template: lapis.j2
  - name: silo
    template: silo.j2

nginx_enabled_sites:
  - wasap-scout
  - lapis
  - silo

Test Configuration¶

For resource-constrained environments, use test variables:

ansible-playbook playbooks/srsilo/update-pipeline.yml -i inventory.ini \
  -e "@playbooks/srsilo/vars/test_vars.yml"

Test vars typically include:

srsilo_docker_memory_limit: 8g
srsilo_fetch_max_reads: 5000000
srsilo_chunk_size: 30000