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skill#

List, show, or manage expert knowledge profiles for bioinformatics tools.

Synopsis#

oxo-call skill list
oxo-call skill show     <TOOL>
oxo-call skill install  <TOOL> [--url <URL>]
oxo-call skill remove   <TOOL>
oxo-call skill create   <TOOL> [-o <FILE>]
oxo-call skill path
oxo-call skill mcp add    <URL> [--name <NAME>] [--api-key <KEY>]
oxo-call skill mcp remove <URL-OR-NAME>
oxo-call skill mcp list
oxo-call skill mcp ping

Description#

Skills are Markdown files with YAML front-matter that inject domain-expert knowledge into the LLM prompt for a specific tool. They contain key concepts, common pitfalls, and worked command examples. When oxo-call finds a matching skill, it includes this knowledge in the prompt, dramatically improving accuracy.

Skills can come from four sources (highest priority first):

  1. User-defined files in ~/.config/oxo-call/skills/
  2. Community-installed files in ~/.local/share/oxo-call/skills/
  3. MCP servers — remote skill providers using the Model Context Protocol
  4. Built-in — compiled into the binary (159 tools)

Subcommands#

skill list#

List all available skills (built-in, community, MCP, and user-defined):

oxo-call skill list

MCP-sourced skills are shown with a yellow mcp:<server-name> label.

skill show#

Display the full skill content for a tool (queries MCP servers if needed):

oxo-call skill show samtools

skill install#

Install a community skill or from a custom URL:

oxo-call skill install bismark
oxo-call skill install mytool --url https://example.com/mytool.md

Both .md (YAML front-matter + Markdown, preferred) and legacy .toml formats are supported.

skill remove#

Remove a community or user-installed skill:

oxo-call skill remove mytool

skill create#

Generate a skill Markdown template:

oxo-call skill create mytool
oxo-call skill create mytool -o ~/.config/oxo-call/skills/mytool.md

skill path#

Show the user skills directory path:

oxo-call skill path

skill mcp add#

Register an MCP skill provider server:

oxo-call skill mcp add http://localhost:3000
oxo-call skill mcp add http://localhost:3000 --name local-skills
oxo-call skill mcp add https://skills.example.org --name org-skills --api-key token

skill mcp remove#

Unregister an MCP server by URL or name:

oxo-call skill mcp remove local-skills
oxo-call skill mcp remove http://localhost:3000

skill mcp list#

List all registered MCP skill servers:

oxo-call skill mcp list

skill mcp ping#

Test connectivity to all registered servers and report their skill count:

oxo-call skill mcp ping

Skill Load Priority#

  1. User-defined: ~/.config/oxo-call/skills/<tool>.md (.toml also accepted)
  2. Community-installed: ~/.local/share/oxo-call/skills/<tool>.md (.toml also accepted)
  3. MCP servers: Configured via skill mcp add — see MCP Skill Provider
  4. Built-in: Compiled into the binary

Skill File Format#

Skills use a Markdown file with YAML front-matter:

---
name: mytool
category: alignment
description: One-line description of the tool
tags: [bam, sam, ngs]
author: your-name   # optional
source_url: https://tool-docs.example.com   # optional
---

## Concepts

- Key concept 1 about the tool
- Key concept 2 about the tool

## Pitfalls

- Common mistake 1 and how to avoid it
- Common mistake 2 and how to avoid it

## Examples

### description of what to do
**Args:** `--flag1 --flag2 input output`
**Explanation:** why these flags were chosen

Built-in Skill Coverage#

oxo-call ships with 159 built-in skills covering all major omics domains. See Skill System Reference for the full list.