skills-hub
- Repo stars 378
- Author updated Live
- Author repo BioClaw
- Domain
- Other
- Compatible agents
-
- Claude Code
- Cursor
- Cline
- Codex
- Windsurf
- Gemini CLI
- +20
- Trust score
- 88 / 100 · community maintained
- Author / version / license
- @Runchuan-BU · no license declared
- Token usage
- Lean
- Setup complexity
- Guided setup
- External API key
- Not required
- Operating systems
- Unspecified (assume cross-platform)
- Runtime requirements
- Python
- Permissions
-
- Read-only
- Write / modify
- Shell exec
- Network behavior
- External requests
- Install commands
- 26 variants
Profile is derived at build time from SKILL.md and install vectors. Subject to drift from author intent.
Heads up: 未限定 allowed-tools，默认拥有全部工具权限。
---
name: skills-hub
description: Browse and install community skills from the BioClaw Skills Hub. Use when a user's task is not c…
category: other
runtime: Python
---
# skills-hub output preview
## PART A: Task fit
- Use case: 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"..
- Inputs: target material, constraints, expected output, and acceptance criteria.
- Evidence boundary: follow “When to Use / Hub Structure / How to Execute” and do not present inference as author intent.
## PART B: Execution result
- **01** The card summarizes the use case; runtime output centers on “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".”.
- **02** When the source has headings, the agent prioritizes “When to Use / Hub Structure / How to Execute” so the result follows the author’s structure.
- **03** Typical output includes task judgment, concrete steps, required commands or file edits, validation, and follow-up options.
- **04** Risk context follows the fingerprint: read files, write/modify files, run shell commands; may access external network resources; usually needs no extra API key.
## Running Rules
- read files, write/modify files, run shell commands; may access external network resources; usually needs no extra API key.
- Validate with a small sample before expanding scope.
- Return the result, validation criteria, and next iteration options.The source mentions slash commands such as `/workspace`; use them first when your agent supports command triggers.
Name target files or source material, expected output, forbidden changes, and whether network or shell access is allowed. Permission fingerprint: read files, write/modify files, run shell commands.
Start with a small task and check whether the result follows “When to Use / Hub Structure / How to Execute”. Inspect diffs, logs, previews, or tests before expanding scope.
Confirm the final output includes a concrete result, evidence, and next action. If it stays generic, tighten inputs, boundaries, and acceptance criteria.
---
name: skills-hub
description: Browse and install community skills from the BioClaw Skills Hub. Use when a user's task is not c…
category: other
source: Runchuan-BU/BioClaw
---
# skills-hub
## When to use
- Browse and install community skills from the BioClaw Skills Hub. Use when a user's task is not covered by built-in ski…
- Use it when the task has clear inputs, repeatable steps, and validation criteria.
## What to provide
- Target material, scope, expected result, and forbidden changes.
- Whether network, commands, file writes, or external services are allowed.
## Execution rules
- Organize steps around “When to Use / Hub Structure / How to Execute” and keep inference separate from source facts.
- read files, write/modify files, run shell commands; may access external network resources; usually needs no extra API key.
- Validate with a small sample before expanding the task.
## Output requirements
- Return the deliverable, key evidence, validation method, and next action.
- Mark missing information as unknown; do not invent commands, platforms, or dependencies.The author source anchors workflow facts; repository files anchor sources and commands; Fluxly only adds fit, limitations, and quality judgment.
skill "skills-hub" {
input -> user goal + target files + boundaries + acceptance criteria
context -> When to Use / Hub Structure / How to Execute
rules -> SKILL.md triggers / order / output contract
runtime -> Python | read files, write/modify files, run shell commands | may access external network resources
guardrails -> usually needs no extra API key + small-sample validation + diff/log review
output -> copyable result + checklist + next iteration
}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/nullStep 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
Decide Fit First
Design Intent
How To Use It
Boundaries And Review