Agent Skills › Runchuan-BU/BioClaw › skills-hub

skills-hub

GitHub

用于浏览和安装BioClaw社区技能库中的专业生物信息学技能，支持查找未内置的特定分析流程、查询可用技能及执行复杂流水线任务。

container/skills/skills-hub/SKILL.md Runchuan-BU/BioClaw

Trigger Scenarios

用户请求内置技能未覆盖的分析任务询问有哪些其他可用技能或是否有某项技能的实现需要特殊的分析流水线（如蛋白质设计、EHR分析等）

Install

npx skills add Runchuan-BU/BioClaw --skill skills-hub -g -y

More Options

Non-standard path

npx skills add https://github.com/Runchuan-BU/BioClaw/tree/main/container/skills/skills-hub -g -y

Use without installing

npx skills use Runchuan-BU/BioClaw@skills-hub

指定 Agent (Claude Code)

npx skills add Runchuan-BU/BioClaw --skill skills-hub -a claude-code -g -y

安装 repo 全部 skill

npx skills add Runchuan-BU/BioClaw --all -g -y

预览 repo 内 skill

npx skills add Runchuan-BU/BioClaw --list

SKILL.md

Frontmatter

{
    "name": "skills-hub",
    "description": "Browse and install community skills from the BioClaw Skills Hub. Use when a user's task is not covered by built-in skills, or when the user asks about available skills, advanced workflows, or specialized analysis pipelines. Triggers on \"skills hub\", \"more skills\", \"install skill\", \"community skills\", \"find a skill for\"."
}

Skills Hub Browser

Search, browse, and install community-contributed skills from the BioClaw Skills Hub.

The Hub contains 70+ specialized bioinformatics skills organized into domains. Skills downloaded from the Hub are cached locally so they persist for the rest of the session.

When to Use

User requests an analysis not covered by the built-in skills listed in your system prompt
User asks "what other skills are available" or "do you have a skill for X"
User needs a specialized pipeline (e.g., protein design, EHR analysis, spatial transcriptomics workflows beyond the built-in)

Hub Structure

The Hub organizes skills into these domains:

Domain	Examples
`core-bioinformatics`	alignment-and-mapping, read-qc, sequence-io, database-access
`transcriptomics`	bulk-rna-expression, differential-expression
`single-cell-and-spatial`	scrna-preprocessing, spatial-transcriptomics, cell-annotation
`epigenomics-and-regulation`	atac-seq, chip-seq, dna-methylation
`genomics-and-variation`	variant-calling, genome-assembly, long-read-genomics
`metagenomics-and-microbiome`	metagenomics, phylogenetics, microbial-community
`proteomics-and-metabolomics`	mass-spec, metabolomics
`multi-omics-and-systems`	multi-omics-integration, pathway-analysis
`protein-design`	alphafold2-multimer, proteinmpnn, rfdiffusion, boltzgen
`ehr-analysis`	electronic health record analysis

How to Execute

Step 1: Fetch the taxonomy (skill index)

curl -sL "https://raw.githubusercontent.com/zongtingwei/Bioclaw_Skills_Hub/main/catalog/taxonomy.yaml"

This returns the full skill catalog organized by domain. Use it to find the skill name that matches the user's need.

Step 2: List skills in a specific domain

curl -sL "https://api.github.com/repos/zongtingwei/Bioclaw_Skills_Hub/contents/skills/<domain>" | python3 -c "
import json, sys
for item in json.load(sys.stdin):
    if item['type'] == 'dir':
        print(item['name'])
"

Replace <domain> with a domain name from the table above.

Step 3: Download and read a skill

# Download the SKILL.md
DOMAIN="<domain>"
SKILL="<skill-name>"
CACHE_DIR="/workspace/group/.hub-skills/${SKILL}"
mkdir -p "${CACHE_DIR}"
curl -sL "https://raw.githubusercontent.com/zongtingwei/Bioclaw_Skills_Hub/main/skills/${DOMAIN}/${SKILL}/SKILL.md" \
  -o "${CACHE_DIR}/SKILL.md"

Then read the downloaded skill:

read_file({ file_path: "/workspace/group/.hub-skills/<skill-name>/SKILL.md" })

Step 4: Install dependencies (if needed)

Some Hub skills require extra Python packages. Check the SKILL.md for a "Preferred Tools" or "Dependencies" section. Install with:

pip install <package> --quiet 2>/dev/null

Step 5: Execute the skill

Follow the workflow described in the downloaded SKILL.md, just like any built-in skill.

Important Notes

Always check built-in skills first before fetching from the Hub
Downloaded skills are cached in /workspace/group/.hub-skills/ for the session
The Hub is a community resource — skills may reference tools not installed in the container; install them with pip/apt as needed
If GitHub is unreachable, inform the user and suggest using built-in skills instead