bio-foundation-housekeeping
Initialize a bioinformatics project scaffold with reproducible environments, schemas, and data cataloging. Use for new projects or repo setup.
npx skills add BioTender-max/awesome-bio-agent-skills --skill bio-foundation-housekeeping --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Bio Foundation Housekeeping Initialize a bioinformatics project scaffold with reproducible environments, schemas, and data cataloging. Use for new projects or repo setup. ## Instructions 1. Create standard directory layout (data/, results/, schemas/, workflows/, src/, notebooks/). 2. Initialize Pixi workspace and lockfile; define tasks. 3. Define LinkML schemas and generate Pydantic models. 4. Create DuckDB catalog and register parquet tables. ## Quick Reference | Task | Action | |------|--------| | Run workflow | Follow the steps in this skill and capture outputs. | | Validate inputs | Confirm required inputs and reference data exist. | | Review outputs | Inspect reports and QC gates before proceeding. | | Tool docs | See `docs/README.md`. | ## Input Requirements Prerequisites: - Tools available in the active environment (Pixi/conda/system). See `docs/README.md` for expected tools. - Target project root is writable. Inputs: - project root (path) - metadata schema requirements - workflow engine preference (optional) ## Output - pixi.toml - pixi.lock - schemas/ - data/catalog.duckdb - results/bio-foundation-housekeeping/report.md - results/bio-foundation-housekeeping/logs/ ## Qual
- Instructions
- Quick Reference
- Input Requirements
- Output
- Quality Gates
- Examples
- Example 1: Expected input layout
- Troubleshooting
What does the bio-foundation-housekeeping skill do?
Initialize a bioinformatics project scaffold with reproducible environments, schemas, and data cataloging. Use for new projects or repo setup.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill bio-foundation-housekeeping --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.