Initial release: rarelens platform skeleton (AGPL-3.0)

End-to-end variant interpretation platform for rare genetic disease research:
SvelteKit UI, FastAPI + PostgreSQL API, Nextflow/Ensembl VEP pipeline,
LightGBM pathogenicity scoring with MLflow, K8s/ArgoCD/GCP infrastructure.
Public test data only; no clinical claims.

docker-compose.yml

@@ -0,0 +1,45 @@
+services:
+  db:
+    image: postgres:16-alpine
+    environment:
+      POSTGRES_USER: rarelens
+      POSTGRES_PASSWORD: rarelens
+      POSTGRES_DB: rarelens
+    ports: ["5432:5432"]
+    volumes: [pgdata:/var/lib/postgresql/data]
+    healthcheck:
+      test: ["CMD-SHELL", "pg_isready -U rarelens"]
+      interval: 5s
+      retries: 10
+
+  api:
+    build: ./api
+    environment:
+      DATABASE_URL: postgresql+asyncpg://rarelens:rarelens@db:5432/rarelens
+      MLFLOW_TRACKING_URI: http://mlflow:5000
+    ports: ["8000:8000"]
+    depends_on:
+      db: { condition: service_healthy }
+    volumes: ["./api:/app"]
+    command: uvicorn app.main:app --host 0.0.0.0 --port 8000 --reload
+
+  web:
+    build:
+      context: ./web
+      target: build
+    environment:
+      PUBLIC_API_URL: http://localhost:8000
+    ports: ["5173:5173"]
+    depends_on: [api]
+    volumes: ["./web:/app", "/app/node_modules"]
+    command: npm run dev -- --host
+
+  mlflow:
+    image: ghcr.io/mlflow/mlflow:v2.16.0
+    command: mlflow server --host 0.0.0.0 --backend-store-uri sqlite:///mlflow.db --default-artifact-root /mlruns
+    ports: ["5000:5000"]
+    volumes: [mlruns:/mlruns]
+
+volumes:
+  pgdata:
+  mlruns: