majiayu000 Bio Foundation Housekeeping
When to use
- Initialize a bioinformatics project scaffold with reproducible environments, schemas, and data cataloging. Use for new projects or repo setup.
Prerequisites
- Tools installed via pixi (see pixi.toml).
- Target project root is writable.
Inputs
- project root (path)
- metadata schema requirements
- workflow engine preference (optional)
Outputs
- pixi.toml
- pixi.lock
- schemas/
- data/catalog.duckdb
- results/bio-foundation-housekeeping/report.md
- results/bio-foundation-housekeeping/logs/
Steps
- Create standard directory layout (data/, results/, schemas/, workflows/, src/, notebooks/).
- Initialize Pixi workspace and lockfile; define tasks.
- Define LinkML schemas and generate Pydantic models.
- Create DuckDB catalog and register parquet tables.
QC gates
- Schema generation succeeds and models are importable.
- pixi.lock is created and consistent with pixi.toml.
- DuckDB catalog is readable.
- On failure: retry with alternative parameters; if still failing, record in report and exit non-zero.
Validation
- Verify project root exists and is writable.
- Validate generated schemas against expected fields.
Tools
- pixi v0.43.0
- linkml v1.9.6
- pydantic v2.12.5
- duckdb v1.4.3
Paper summaries (2023-2025)
- summaries/ (include example use cases and tool settings used)
Tool documentation
- Pixi - Package and environment management
- LinkML - Data modeling and schema generation
- Pydantic - Data validation using Python type hints
- DuckDB - In-process analytical database
References
- See ../bio-skills-references.md