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bio-foundation-housekeeping

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Initialize a bioinformatics project scaffold with reproducible environments, schemas, and data cataloging. Use for new projects or repo setup.

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How to use this skill

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  1. Open your project in Codex.
  2. Copy the prompt below and paste it into your agent.
  3. Review the proposed files and risks before you approve installation.
Prompt to paste
I want to install this Agent Skill for this project in Codex.

Source SKILL.md: https://github.com/majiayu000/claude-skill-registry/blob/HEAD/skills/data/bio-foundation-housekeeping/SKILL.md

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First, summarize what it does, its dependencies, license status if identifiable, and any risks. Show the exact files you propose to add under .agents/skills/bio-foundation-housekeeping/. Do not write files or run scripts until I approve.

After I approve, install the complete skill folder, including required referenced files, into that project location. Verify it is discoverable, then tell me its actual invocation name and how to use it. Do not claim it is installed until you have verified it.

Copying this prompt does not install or run the skill. Review third-party files before use. Codex skill guide

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

  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.

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