docs/mkdocs.yml at main · ClawBio/docs · GitHub

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site_name: ClawBio Documentation
site_url: https://docs.clawbio.ai
site_description: Technical documentation, tutorials, and skill reference for ClawBio, the bioinformatics-native AI agent skill library.
site_author: Manuel Corpas
repo_url: https://github.com/ClawBio/ClawBio
repo_name: ClawBio/ClawBio

theme:
  name: material
  favicon: assets/favicon.ico
  logo: assets/clawbio-logo.jpeg
  custom_dir: overrides
  palette:
    - scheme: clawbio
      primary: custom
      accent: custom
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
    - scheme: default
      primary: green
      accent: green
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
  features:
    - navigation.tabs
    - navigation.tabs.sticky
    - navigation.top
    - navigation.footer
    - search.suggest
    - content.code.copy
    - header.autohide
  font: false

nav:
  - Home: index.md
  - Berlin 2026:
    - The Event: hackathon/berlin/index.md
    - Setup: hackathon/berlin/setup.md
    - Nebius Quickstart: hackathon/berlin/nebius-quickstart.md
    - Challenges: hackathon/berlin/tracks.md
    - Challenge Data: hackathon/berlin/data/index.md
  - Skills:
    - Skill Library: skills/index.md
    - PharmGx Reporter: skills/pharmgx-reporter.md
    - scRNA Orchestrator: skills/scrna-orchestrator.md
    - Equity Scorer (HEIM): skills/equity-scorer.md
    - NutriGx Advisor: skills/nutrigx-advisor.md
    - Genome Compare: skills/genome-compare.md
    - GWAS PRS: skills/gwas-prs.md
    - GWAS Lookup: skills/gwas-lookup.md
    - Galaxy Bridge: skills/galaxy-bridge.md
    - RNA-seq DE: skills/rnaseq-de.md
  - Tutorials:
    - Try Conversational Genome: tutorials/conversational-genome.md
    - Ask ClawBio in your browser: tutorials/ask-clawbio.md
    - Overview: tutorials/index.md
    - Basics:
      - Setup: tutorials/setup.md
      - Penguins Analysis: tutorials/penguins-analysis.md
      - Journal Club Slides: tutorials/journal-club-slides.md
      - Single Cell Portal: tutorials/single-cell-portal.md
      - Context Management: tutorials/context-management.md
      - APM: tutorials/apm.md
    - Extras:
      - Rules and Memory: tutorials/rules.md
      - GitHub Education: tutorials/github-education.md
      - Building Custom Agents: tutorials/making-agents.md
      - tmux Sessions: tutorials/tmux-sessions.md
      - Telegram Bot: tutorials/telegram-bot.md
    - ClawBio:
      - "Step 1 — Run Your First Skill": tutorials/run-your-first-skill.md
      - "Step 2 — Build a Skill": tutorials/build-a-skill.md
      - "Step 3 — Variant Interpretation": tutorials/variant-interpretation-workshop.md
      - "Step 4 — GWAS Workshop": tutorials/gwas-workshop.md
      - "Step 5 — 30x WGS Workshop": tutorials/30x-wgs-workshop.md
  - Deployment:
    - Overview: deployment/index.md
    - Docker: deployment/docker.md
    - Railway: deployment/railway.md
    - Private Cloud: deployment/private-cloud.md
  - Reference:
    - SKILL.md Spec: reference/skillmd-spec.md
    - CLI: reference/cli.md
    - MCP Server (deprecated): reference/mcp.md
    - Security: reference/security.md
    - Contributing: contributing/index.md
  - Presentations: presentations/index.md
  - Hackathon:
    - Guide: hackathon/index.md
    - Setup: hackathon/setup.md
    - Build a Skill: hackathon/first-skill.md
    - Add Python: hackathon/add-python.md
    - Submit: hackathon/submit.md
    - Agentic Tools: hackathon/agentic-tools.md

plugins:
  - search

markdown_extensions:
  - admonition
  - pymdownx.details
  - pymdownx.superfences
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.keys
  - pymdownx.snippets
  - tables
  - attr_list
  - md_in_html
  - toc:
      permalink: true

extra_css:
  - stylesheets/clawbio.css

extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/ClawBio/ClawBio
    - icon: fontawesome/brands/discord
      link: https://discord.gg/clawbio
  generator: false

copyright: "&copy; 2026 ClawBio — Research and educational tool. Not a medical device."