skills-hub

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

[!note] Vault audit 2026-07-24 — USE-10 Use this to browse/install bioinformatics community skills from the BioClaw Skills Hub; for discovering skills across the general skill ecosystem use find-skills. Distinguishing axis: bio/BioClaw domain vs general ecosystem.

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 (nested under protein-design/skills/)
ehr-analysis	electronic health record analysis (single SKILL.md, no per-skill directory)

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: Resolve the SKILL.md path

Domains do not share one on-disk layout, so never build the path from a template. protein-design nests its skills under skills/protein-design/skills/<skill>/SKILL.md and ehr-analysis is a single file at skills/ehr-analysis/SKILL.md, while the other eight domains use skills/<domain>/<skill>/SKILL.md. Read the real path out of the repository tree:

curl -sL "https://api.github.com/repos/zongtingwei/Bioclaw_Skills_Hub/git/trees/main?recursive=1" \
  | python3 -c "
import json, sys
tree = json.load(sys.stdin)
paths = [t['path'] for t in tree['tree'] if t['path'].endswith('SKILL.md')]
for p in paths:
    print(p)
"

Filter that list for the skill you want. To list the skills in one domain, keep the paths under skills/<domain>/ and take the directory that immediately precedes SKILL.md.

Step 3: Download and read a skill

# SKILL_PATH is the repo-relative path resolved in Step 2, e.g.
#   skills/single-cell-and-spatial/cell-annotation/SKILL.md
#   skills/protein-design/skills/alphafold2-multimer/SKILL.md
#   skills/ehr-analysis/SKILL.md
SKILL_PATH="<path from step 2>"
SKILL="<skill-name>"
CACHE_DIR="/workspace/group/.hub-skills/${SKILL}"
mkdir -p "${CACHE_DIR}"
curl -fsSL "https://raw.githubusercontent.com/zongtingwei/Bioclaw_Skills_Hub/main/${SKILL_PATH}" \
  -o "${CACHE_DIR}/SKILL.md"

curl -f makes a 404 fail loudly instead of caching GitHub's error page as the skill.

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