| 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
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
