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claude-codescience

Claude-skill-registry bio-foundation-housekeeping

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

install
source · Clone the upstream repo
git clone https://github.com/majiayu000/claude-skill-registry
Claude Code · Install into ~/.claude/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/majiayu000/claude-skill-registry "$T" && mkdir -p ~/.claude/skills && cp -r "$T/skills/data/bio-foundation-housekeeping" ~/.claude/skills/majiayu000-claude-skill-registry-bio-foundation-housekeeping && rm -rf "$T"
manifest: skills/data/bio-foundation-housekeeping/SKILL.md
tags
#bioinformatics#project-setup#schema-generation#environment-management#data-cataloging
source content

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