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

@@ -0,0 +1,9 @@
+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

@@ -0,0 +1,4 @@
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+namespace: rarelens
+resources: [namespace.yaml, api.yaml, web.yaml, ingress.yaml]

infra/k8s/base/namespace.yaml

@@ -0,0 +1,3 @@
+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 }] }

infra/k8s/overlays/gcp/kustomization.yaml

@@ -0,0 +1,21 @@
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+resources: [../../base]
+images:
+  - { name: rarelens/api, newName: europe-west2-docker.pkg.dev/PROJECT/rarelens/api, newTag: latest }
+  - { name: rarelens/web, newName: europe-west2-docker.pkg.dev/PROJECT/rarelens/web, newTag: latest }
+patches:
+  - target: { kind: ServiceAccount, name: rarelens-api }
+    patch: |
+      - op: add
+        path: /metadata/annotations
+        value: { iam.gke.io/gcp-service-account: [email protected] }
+  - target: { kind: Deployment, name: api }
+    patch: |
+      - op: add
+        path: /spec/template/spec/containers/-
+        value:
+          name: cloud-sql-proxy
+          image: gcr.io/cloud-sql-connectors/cloud-sql-proxy:2.13.0
+          args: ["--structured-logs", "--port=5432", "PROJECT:europe-west2:rarelens-pg"]
+          securityContext: { runAsNonRoot: true }

infra/k8s/overlays/local/kustomization.yaml

@@ -0,0 +1,9 @@
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+resources: [../../base, postgres.yaml]
+images:
+  - { name: rarelens/api, newName: rarelens-api, newTag: dev }
+  - { name: rarelens/web, newName: rarelens-web, newTag: dev }
+secretGenerator:
+  - name: api-secrets
+    literals: [DATABASE_URL=postgresql+asyncpg://rarelens:rarelens@postgres:5432/rarelens]

infra/k8s/overlays/local/postgres.yaml

@@ -0,0 +1,20 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata: { name: postgres }
+spec:
+  selector: { matchLabels: { app: postgres } }
+  template:
+    metadata: { labels: { app: postgres } }
+    spec:
+      containers:
+        - name: postgres
+          image: postgres:16-alpine
+          env:
+            - { name: POSTGRES_USER, value: rarelens }
+            - { name: POSTGRES_PASSWORD, value: rarelens }
+            - { name: POSTGRES_DB, value: rarelens }
+---
+apiVersion: v1
+kind: Service
+metadata: { name: postgres }
+spec: { selector: { app: postgres }, ports: [{ port: 5432 }] }