Agent skill

Skill Builder

by ClawBio in ClawBio/ClawBio

Scaffold a new ClawBio skill from a spec file (JSON/YAML) or interactively — generates SKILL.md, Python skeleton, tests, and updates catalog.json

MITAuto-check passedAgent Workflows

Install Skill Builder

skills CLI
$ npx skills add ClawBio/ClawBio --skill skill-builder -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install ClawBio/ClawBio skill-builder --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/skill-builder .claude/skills/skill-builder && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
skill-builder
GitHub stars
1.2k
Used in
1 other repo
Token cost
~2.1k tokens
SKILL.md length
647 words
Files
5
Skills in repo
104
Repo updated
First seen
Licence
MIT

At a glance

Scaffold a new ClawBio skill from a spec file (JSON/YAML) or interactively — generates SKILL.md, Python skeleton, tests, and updates catalog.json

  • Works in 5 steps: Spec-driven scaffolding: Read a JSON (or… → Interactive mode: Prompt for skill… → Validation: Check any existing SKILL.md… → …
  • Tasks that involve Skill authoring
  • SKILL.md covers Why This Exists, Core Capabilities, Input Formats and Workflow, plus 10 more sections
  • Runs Python scripts from its folder; calls python

What it does

Skill Builder is an agent skill from ClawBio/ClawBio. Scaffold a new ClawBio skill from a spec file (JSON/YAML) or interactively — generates SKILL.md, Python skeleton, tests, and updates catalog.json

Its SKILL.md is about 2.1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 6 other files (for example `demo_spec.json`, `skill_builder.py` and `templates/spec_template.json`).

It sits in Agent Workflows, covering Skill authoring. It works with Python. The repository describes itself as: 🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free. The licence is MIT.

When your agent uses it

  • Tasks that involve Skill authoring

Example prompts

  • “/skill-builder”

Requirements

  • Python 3

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

  1. Spec-driven scaffolding: Read a JSON (or YAML with pyyaml) spec file and generate a complete skill directory.
  2. Interactive mode: Prompt for skill details when no spec file is provided (--interactive).
  3. Validation: Check any existing SKILL.md against the CONTRIBUTING.md checklist (--validate-only).
  4. Auto-registration: Update skills/catalog.json and patch clawbio.py's SKILLS dict when run from inside the ClawBio repo.
  5. Dry-run preview: Print all generated content without writing files (--dry-run).

What it can do on your machine

Read from SKILL.md and the folder at commit 5e045e3. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships script files (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Skill Builder loads about 2.1k tokens when it runs. Until then it costs about 40 tokens; SKILL.md has 647 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~40
When it runs · the whole SKILL.md, loaded when a task matches
~2.1k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from ClawBio/ClawBio at commit 5e045e3, republished under its MIT licence (© ClawBio). 647 words, ~2,090 tokens.

Download SKILL.mdSave it as .claude/skills/skill-builder/SKILL.md (or your agent's skills folder). This skill also uses 4 other files; get the full folder from GitHub.
name
skill-builder
description
Scaffold a new ClawBio skill from a spec file (JSON/YAML) or interactively — generates SKILL.md, Python skeleton, tests, and updates catalog.json
license
MIT
metadata.author
Mj
metadata.tags
meta, scaffolding, developer-tools, skill-creation
metadata.version
0.1.0

🦖 Skill Builder

You are Skill Builder, a specialised ClawBio meta-skill for scaffolding new skills. Your role is to take a skill specification and generate a complete, PR-ready ClawBio skill directory with all required files.

Why This Exists

  • Without it: Contributors must manually copy the template, fill in every section, write a Python skeleton from scratch, and manually update catalog.json and clawbio.py — a 30-60 minute process prone to missing required sections or malformed YAML.
  • With it: Provide a JSON spec and get a complete, validated, immediately runnable skill scaffold in seconds, ready to submit as a pull request.
  • Why ClawBio: The scaffold enforces all requirements from CONTRIBUTING.md automatically — no forgotten sections, no malformed frontmatter, no missing reproducibility bundle.

Core Capabilities

  1. Spec-driven scaffolding: Read a JSON (or YAML with pyyaml) spec file and generate a complete skill directory.
  2. Interactive mode: Prompt for skill details when no spec file is provided (--interactive).
  3. Validation: Check any existing SKILL.md against the CONTRIBUTING.md checklist (--validate-only).
  4. Auto-registration: Update skills/catalog.json and patch clawbio.py's SKILLS dict when run from inside the ClawBio repo.
  5. Dry-run preview: Print all generated content without writing files (--dry-run).

Input Formats

FormatExtensionRequired FieldsExample
JSON spec.jsonname, description, authorspec.json
YAML spec.yaml / .ymlname, description, authorspec.yaml (requires pyyaml)
Existing SKILL.md.mdAny SKILL.mdUsed with --validate-only

Workflow

When the user asks to create a new skill:

  1. Load spec: Read JSON/YAML spec file, or collect fields interactively if --interactive
  2. Validate spec: Check required fields (name, description, author); apply defaults for optional fields
  3. Generate files: Create SKILL.md, <name>.py, tests/test_<name>.py, examples/example_spec.json
  4. Update registry: If repo root found, append entry to catalog.json and patch the SKILLS dict in clawbio/cli.py (falls back to clawbio.py in older checkouts)
  5. Report: Print a summary of generated files and next steps

CLI Reference

bash
# Spec-driven (recommended for agents)
python skills/skill-builder/skill_builder.py --input spec.json --output skills/my-skill/

# Interactive (human-friendly)
python skills/skill-builder/skill_builder.py --interactive

# Demo (scaffolds hello-bioinformatics skill)
python skills/skill-builder/skill_builder.py --demo --output /tmp/skill_builder_demo

# Validate an existing SKILL.md
python skills/skill-builder/skill_builder.py --validate-only --input skills/my-skill/SKILL.md

# Dry run (print without writing)
python skills/skill-builder/skill_builder.py --input spec.json --dry-run

# Via ClawBio runner
python clawbio.py run skill-builder --demo
python clawbio.py run skill-builder --input spec.json

Demo

bash
python clawbio.py run skill-builder --demo

Expected output: A fully scaffolded hello-bioinformatics skill at /tmp/skill_builder_demo/hello-bioinformatics/ — includes SKILL.md, hello_bioinformatics.py, tests/test_hello_bioinformatics.py, and a result.json + report.md in the skill-builder output directory documenting what was created.

Spec File Reference

Minimal spec (JSON):

json
{
  "name": "my-skill",
  "description": "What this skill does",
  "author": "Your Name"
}

Full spec with all optional fields:

json
{
  "name": "my-skill",
  "description": "One-line description of what this skill does",
  "author": "Your Name",
  "domain": "genomics",
  "capabilities": ["Capability 1", "Capability 2"],
  "trigger_keywords": ["keyword1", "another phrase"],
  "tags": ["tag1", "tag2"],
  "dependencies": {
    "required": ["package >= 1.0"],
    "optional": ["package2"]
  },
  "chaining_partners": ["pharmgx-reporter"],
  "cli_alias": "myskill",
  "input_formats": [
    {
      "format": "23andMe raw data",
      "extension": ".txt",
      "required_fields": "rsid, chromosome, position, genotype",
      "example": "demo_patient.txt"
    }
  ]
}
Show full SKILL.md (304 more words)Show less

Algorithm / Methodology

  1. Parse spec: Load JSON (stdlib) or YAML (pyyaml if available); fall back to interactive prompts
  2. Normalise name: Enforce lowercase-hyphen naming (vcf-annotator, not VCF_Annotator)
  3. Fill defaults: domain → "bioinformatics", version → "0.1.0", capabilities/triggers → generic placeholders
  4. Render SKILL.md: Fill YAML frontmatter + all 13 required body sections from template
  5. Render Python skeleton: argparse wired with --input/--output/--demo; output boilerplate creates report.md, result.json, reproducibility bundle
  6. Render test skeleton: pytest fixture + 4 standard tests (demo, report, result.json, reproducibility bundle)
  7. Validate: Run the 13-item CONTRIBUTING checklist against the generated SKILL.md before writing
  8. Register: Append catalog entry; patch clawbio.py SKILLS dict via targeted string replacement

Example Queries

  • "Create a new skill called vcf-annotator that annotates VCF files with ClinVar"
  • "Scaffold a skill for running PLINK GWAS pipelines"
  • "Build a skill template for GO enrichment analysis"
  • "Validate my SKILL.md before I submit a PR"

Output Structure

output_directory/
├── report.md                   # Summary of what was generated
├── result.json                 # Machine-readable scaffold manifest
└── reproducibility/
    ├── commands.sh             # Exact command to reproduce the scaffold
    ├── environment.yml         # Environment snapshot
    └── checksums.sha256        # SHA-256 of report.md and result.json

Generated skill at skills/<name>/:
├── SKILL.md                    # Complete skill definition
├── <name>.py                   # Python skeleton with --input/--output/--demo
├── tests/
│   └── test_<name>.py          # pytest skeleton with 3 standard tests
└── examples/
    └── example_spec.json       # The spec that generated this skill

Dependencies

Required (stdlib only — zero install):

  • Python 3.11+ standard library (argparse, pathlib, json, re, textwrap, shutil, getpass, socket)

Optional:

  • pyyaml >= 6.0 — enables YAML spec files in addition to JSON; graceful fallback to JSON-only mode if absent

Safety

  • Local-first: No network calls; all generation is offline
  • Non-destructive: Never overwrites existing files without --force; prompts or errors if destination exists
  • No hallucinated science: All generated SKILL.md content is taken directly from the spec; placeholder text is clearly marked with TODO:
  • Audit trail: result.json and the reproducibility bundle record exactly what was generated and when

Integration with Bio Orchestrator

Trigger conditions — the orchestrator routes here when:

  • User says "create a skill", "scaffold a skill", "new skill", "build a skill", "add a skill"
  • User provides a JSON/YAML file with name, description, author fields and asks to build a skill

Chaining partners:

  • bio-orchestrator: Skill builder output feeds back into the orchestrator once registered

Citations

© ClawBio, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 4 other files in skills/skill-builder of ClawBio/ClawBio.

  • SKILL.md
  • demo_spec.json
  • skill_builder.py
  • templates/spec_template.json
  • tests/test_skill_builder.py

Open the folder on GitHubat commit 5e045e3

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in ClawBio/ClawBio, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Skill Builder next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Skill Builder compared with similar skills
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Skill Builder this skillClawBio/ClawBio1.2k1 repos~2.1kAutomated safety check: PassMIT
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DBS Skill Makerdontbesilent2025/dbskill11k—~1.2kAutomated safety check: PassCustom licence
Skill Creatorluongnv89/asm953—~5.3kAutomated safety check: PassMIT
Run History Skill Builderdongshuyan/compass-skills751—~1.8kAutomated safety check: PassMIT
Skill Contract Reviewerrohitg00/ai-engineering-from-scratch66k1 repos~450Automated safety check: PassMIT

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Works with

Categories

Questions about Skill Builder

What does Skill Builder do?

Scaffold a new ClawBio skill from a spec file (JSON/YAML) or interactively — generates SKILL.md, Python skeleton, tests, and updates catalog.json. Skill Builder is an agent skill from ClawBio/ClawBio.

When should I use Skill Builder?

Skill Builder fits situations like: tasks that involve Skill authoring.

How do I install Skill Builder in Claude Code?

Run `npx skills add ClawBio/ClawBio --skill skill-builder -a claude-code`. Or copy the skill folder (skills/skill-builder in ClawBio/ClawBio) into .claude/skills/skill-builder in your project. Claude Code loads it when a task matches its description.

How do I install Skill Builder in Codex?

Run `npx skills add ClawBio/ClawBio --skill skill-builder -a codex`. Or copy the skill folder (skills/skill-builder in ClawBio/ClawBio) into .agents/skills/skill-builder in your project. Codex loads it when a task matches its description.

Can I use Skill Builder in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add ClawBio/ClawBio --skill skill-builder -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/skill-builder, .gemini/skills/skill-builder, .github/skills/skill-builder and .opencode/skills/skill-builder in your project.

What does Skill Builder need to run?

Going by SKILL.md and its folder, Skill Builder needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Skill Builder access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Skill Builder safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Skill Builder use?

Skill Builder is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Skill Builder use?

About 2.1k tokens (SKILL.md is roughly 8.4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Skill Builder?

Skills that share tags, products or a category with Skill Builder: SkillAnything Skill Generator (AgentSkillOS/SkillAnything, 471 stars), DBS Skill Maker (dontbesilent2025/dbskill, 11k stars), Skill Creator (luongnv89/asm, 953 stars) and Run History Skill Builder (dongshuyan/compass-skills, 751 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Skill Builder?

ClawBio (a GitHub organization) maintains it in ClawBio/ClawBio, which has 1,154 GitHub stars. The repository holds 104 skills in this directory. The repository was last updated on October 7, 2026.

Source: ClawBio/ClawBio on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.