skills/quarto-book-setup/SKILL.md
Initialize a new Quarto book project with GitHub Pages. Use when creating a new documentation site, tutorial, or book.
npx skillsauth add musserlab/lab-claude-skills quarto-book-setupInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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When the user invokes /quarto-book-setup, scaffold a new Quarto book project.
Ask the user:
project-name/
├── _quarto.yml
├── index.qmd
├── .gitignore
├── .claude/
│ └── CLAUDE.md
├── PLAN.md
├── README.md
├── images/
└── chapters/ # or use part1/, part2/ structure
└── intro.qmd
project:
type: book
output-dir: _book
execute:
freeze: auto
book:
title: "BOOK_TITLE"
author: "AUTHOR"
date: today
date-format: "MMMM YYYY"
chapters:
- index.qmd
- chapters/intro.qmd
format:
html:
theme:
light: cosmo
dark: darkly
toc: true
code-copy: true
_book/
_site/
.quarto/
*.quarto_ipynb
.DS_Store
.Rhistory
.RData
If user wants GitHub hosting:
git initgh repo create ORG/REPO --public --source=. --pushquarto publish gh-pages --no-promptCreate .claude/CLAUDE.md with:
/publish)/done — see that skill for format)Tell the user:
path/to/projectquarto preview/publishdevelopment
Phylogenetic tree visualization and formatting with ggtree (R) or iTOL (web). Use when rendering a phylogenetic tree as a figure, choosing tree layout, coloring branches or labels by taxonomy, collapsing clades, displaying support values, or adding overlays to a tree. Do NOT load for tree inference (use protein-phylogeny skill) or domain annotation (future separate skill).
development
Configure and manage Claude Code security protections for sensitive files, credentials, and data. Use when the user invokes /security-setup to set up or modify protections against unauthorized file access, credential exposure, or sensitive data leaks.
development
Script organization for data science analysis projects with numbered scripts, data/outs/ directories, and reproducibility conventions. Use when creating new analysis scripts in projects that follow data science conventions (numbered XX_ prefix scripts, outs/ directories, BUILD_INFO.txt). Do NOT load for documentation projects (Quarto books), infrastructure repos, or projects without data/outs/ directory structure.
testing
R renv package management for data science projects. Use when working with renv (renv.lock, renv::restore, renv::snapshot) in R analysis projects. Do NOT load for projects that do not use R or renv.