This page was composed with the aid of generative artificial intelligence; it is partially curated.

High-level

The system is a docker compose stack centered on a core FastAPI app with supporting bioinformatics and visualization services. Key components:

  • FastAPI app (app): Web UI and API, orchestrates PGx operations.

  • PostgreSQL (db): Main database.

  • PharmCAT (pharmcat): API wrapper around PharmCAT JAR for phenotype/report generation.

  • GATK API (gatk-api): Wrapper around GATK tooling.

  • PyPGx (pypgx): Service exposing PyPGx-based calling for supported genes.

  • HAPI FHIR (fhir-server): External FHIR server for EHR integration.

  • Nextflow runner (nextflow): Orchestrates pipelines; mounts the project workspace.

  • Kroki + Mermaid (kroki, mermaid): Renders diagrams (Mermaid, Graphviz, etc.).

  • Genome downloader (genome-downloader): Retrieves reference genomes.

Ports (host → container):

  • App UI/API: ${BIND_ADDRESS:-8765} → 8000

  • DB: 5444 → 5432

  • PharmCAT: 5001 → 5000

  • GATK API: 5002 → 5000

  • PyPGx: 5053 → 5000

  • FHIR: 8090 → 8080

  • Kroki: 8001 → 8000

  • Nextflow runner: 5055 → 5055

  • Docs (this service): 5070 → 8000

Data mounts

Shared host directories used across services:

  • ./data for uploads, reports, and inter-service artifacts

  • ./reference for reference genomes

Workflows

See app/visualizations/workflow.md and app/visualizations/workflow.mmd for diagrams and detailed flows. The app also integrates with Kroki to render diagrams in the UI.

Further Reading

For detailed technical architecture, design principles, and implementation details, see the System Architecture documentation.