skills/quarto-publish/SKILL.md
Commit and publish Quarto project to GitHub Pages. Use when the user wants to publish changes to a Quarto book or website.
npx skillsauth add musserlab/lab-claude-skills publishInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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When the user invokes /publish, commit and publish the Quarto project to GitHub Pages.
git status
If no changes, inform the user and stop.
List the changed files and ask the user for a commit message, or suggest one based on recent work.
git add .
git commit -m "USER_MESSAGE
Co-Authored-By: Claude <[email protected]>"
git push
quarto publish gh-pages --no-prompt
If quarto is not in PATH, try /usr/local/bin/quarto.
Tell the user:
_quarto.yml or git remote)gh-pages branch)quarto publish fails, show the error and suggest troubleshooting stepshttps://ORG.github.io/REPO/development
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.