Skills
.Work. You
Rest

bio-foundation-housekeeping

Community

Establish reproducible bioinformatics projects.

Data & Analytics#workflow#schema#scaffold#bioinformatics#environment#reproducible#data-catalog
Authorfmschulz
Version1.0.0
Installs0

System Documentation

What problem does it solve?

Initialize a reproducible, scalable scaffold for bioinformatics projects including standard directory layout, environment management, data schemas, and cataloging.

Core Features & Use Cases

  • Standardized project layout (data/, results/, schemas/, workflows/, src/, notebooks/) plus a Pixi workspace and locked environments.
  • Generate and integrate LinkML schemas and Pydantic models for metadata validation and data integrity.
  • Build a DuckDB-backed data catalog to enable fast querying of Parquet and CSV datasets in omics workflows.
  • Real-world usage includes starting new studies, onboarding collaborators, and ensuring reproducible analyses and reporting.

Quick Start

Create a new project path and let the scaffold initialize the directories, tooling, and documentation setup for immediate use.

Dependency Matrix

Required Modules

None required

Components

Standard package

💻 Claude Code Installation

Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.

Please help me install this Skill:
Name: bio-foundation-housekeeping
Download link: https://github.com/fmschulz/omics-skills/archive/main.zip#bio-foundation-housekeeping

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
View Source Repository

Agent Skills Search Helper

Install a tiny helper to your Agent, search and equip skill from 223,000+ vetted skills library on demand.