Breeding informatics platform for small barley and triticale breeding programs. Built on Breedbase T3, deployed on Azure.
See CLAUDE.md for full architecture and domain context.
| Directory | Owner | Contents |
|---|---|---|
infra/ |
Software engineer | Bicep/ARM IaC templates |
deploy/ |
Software engineer | Docker Compose, nginx, Breedbase config, backup scripts |
migration/ |
Software engineer | Python: Genovix → Breedbase migration scripts |
brapi/ |
Software engineer | Python: BrAPI integration/glue scripts |
r-package/ |
Breeder | R helper package wrapping QBMS |
pipeline/ |
Breeder | R analytical pipeline |
reports/ |
Breeder | Quarto report templates |
shiny/ |
Breeder | R Shiny dashboard |
docs/ |
Both | Runbooks, architecture notes, design docs |
- Linter: ruff —
ruff check . - Formatter: black —
black . - Config in root
pyproject.toml
- Linter: lintr —
lintr::lint_dir(".") - Config in root
.lintr
After cloning:
pip install pre-commit
pre-commit installFor R hooks also run in R:
install.packages("precommit")- Phase 1 — Deploy Breedbase T3, migrate Genovix data, Field Book connection, Quarto reports, R helper package v1
- Phase 2 — RStudio Server, Shiny dashboard, analytical pipeline
- Phase 3 — Gigwa (genomics)