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/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

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+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 }] }