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.

Makefile

@@ -0,0 +1,25 @@
+.PHONY: up down migrate test pipeline kind lint
+
+up:
+	docker compose up -d --build
+
+down:
+	docker compose down -v
+
+migrate:
+	docker compose exec api alembic upgrade head
+
+test:
+	cd api && uv run pytest -q
+	cd web && npm test
+
+lint:
+	cd api && uv run ruff check . && uv run mypy app
+	cd web && npm run check
+
+pipeline:
+	cd pipeline && nextflow run main.nf -profile docker --vcf ../data/example.vcf.gz --outdir results
+
+kind:
+	kind create cluster --name rarelens || true
+	kubectl apply -k infra/k8s/overlays/local