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.

infra/k8s/base/api.yaml

@@ -0,0 +1,26 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata: { name: api }
+spec:
+  replicas: 2
+  selector: { matchLabels: { app: api } }
+  template:
+    metadata: { labels: { app: api } }
+    spec:
+      serviceAccountName: rarelens-api
+      containers:
+        - name: api
+          image: rarelens/api
+          ports: [{ containerPort: 8000 }]
+          envFrom: [{ secretRef: { name: api-secrets } }]
+          readinessProbe: { httpGet: { path: /health, port: 8000 }, periodSeconds: 5 }
+          resources: { requests: { cpu: 250m, memory: 512Mi }, limits: { cpu: "1", memory: 1Gi } }
+---
+apiVersion: v1
+kind: Service
+metadata: { name: api }
+spec: { selector: { app: api }, ports: [{ port: 80, targetPort: 8000 }] }
+---
+apiVersion: v1
+kind: ServiceAccount
+metadata: { name: rarelens-api }

infra/k8s/base/ingress.yaml

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+apiVersion: networking.k8s.io/v1
+kind: Ingress
+metadata: { name: rarelens }
+spec:
+  rules:
+    - http:
+        paths:
+          - { path: /api, pathType: Prefix, backend: { service: { name: api, port: { number: 80 } } } }
+          - { path: /,    pathType: Prefix, backend: { service: { name: web, port: { number: 80 } } } }

infra/k8s/base/kustomization.yaml

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+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+namespace: rarelens
+resources: [namespace.yaml, api.yaml, web.yaml, ingress.yaml]

infra/k8s/base/namespace.yaml

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+apiVersion: v1
+kind: Namespace
+metadata: { name: rarelens }

infra/k8s/base/web.yaml

@@ -0,0 +1,20 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata: { name: web }
+spec:
+  replicas: 2
+  selector: { matchLabels: { app: web } }
+  template:
+    metadata: { labels: { app: web } }
+    spec:
+      containers:
+        - name: web
+          image: rarelens/web
+          ports: [{ containerPort: 3000 }]
+          env: [{ name: PUBLIC_API_URL, value: /api }]
+          resources: { requests: { cpu: 100m, memory: 128Mi }, limits: { cpu: 500m, memory: 256Mi } }
+---
+apiVersion: v1
+kind: Service
+metadata: { name: web }
+spec: { selector: { app: web }, ports: [{ port: 80, targetPort: 3000 }] }