MCP Skill Provider

oxo-call supports the Model Context Protocol (MCP) as a skill source. Any MCP-compatible server that exposes bioinformatics skill resources can act as an organisational or project-scoped skill library, queried automatically when oxo-call looks for a skill.

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What is MCP?

The Model Context Protocol is an open standard (originally from Anthropic, now widely adopted) that lets AI clients connect to external data and tool servers using a uniform JSON-RPC interface. oxo-call uses MCP's resources API to discover and retrieve skill content from remote servers — no new dependencies required (HTTP + JSON are already used by the LLM client).

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Load Priority

When oxo-call looks for a skill it checks sources in this order (highest wins):

Priority	Source	Location
1	User-defined	~/.config/oxo-call/skills/<tool>.md
2	Community-installed	~/.local/share/oxo-call/skills/<tool>.md
3	MCP servers	Registered in config.toml under [mcp]
4	Built-in	Compiled into the binary

MCP skills are only queried when no higher-priority skill is found for the requested tool, keeping latency impact minimal for well-covered tools.

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MCP Server Contract

An MCP server acting as a skill provider must implement three JSON-RPC methods:

initialize

Standard MCP handshake. oxo-call sends its client info and accepts any response conforming to the MCP 2024-11-05 protocol version.

resources/list

Lists available skill resources. oxo-call recognises skill resources in two ways:

1. Preferred — skill:// URI scheme

   {
     "uri": "skill://samtools",
     "name": "samtools",
     "description": "Suite of programs for SAM/BAM/CRAM handling",
     "mimeType": "text/markdown"
   }
   

2. Fallback — text/markdown MIME type Any resource with "mimeType": "text/markdown" is treated as a skill. The resource "name" field is used as the tool name.

resources/read

Returns the Markdown content for a given URI.

// Request
{ "jsonrpc": "2.0", "id": 3, "method": "resources/read",
  "params": { "uri": "skill://samtools" } }

// Response
{ "jsonrpc": "2.0", "id": 3,
  "result": { "contents": [{ "uri": "skill://samtools",
                              "text": "---\nname: samtools\n...",
                              "mimeType": "text/markdown" }] } }

The text field must contain valid oxo-call skill Markdown (YAML front-matter followed by ## Concepts, ## Pitfalls, and ## Examples sections). Legacy TOML format is also accepted as a fallback.

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Transport

oxo-call uses stateless HTTP POST (no SSE session required):

POST <server-url>/mcp HTTP/1.1
Content-Type: application/json
Accept: application/json
MCP-Protocol-Version: 2024-11-05
Authorization: Bearer <api-key>   # only if api_key is configured

{"jsonrpc":"2.0","id":1,"method":"initialize","params":{...}}

If the server URL already ends in /mcp, it is used as-is; otherwise /mcp is appended automatically.

Timeout: 5 seconds per request. Network errors are silently ignored (the next source in the priority chain is tried).

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Configuration

Register MCP servers in ~/.config/oxo-call/config.toml:

[[mcp.servers]]
url  = "http://localhost:3000"
name = "local-skills"

[[mcp.servers]]
url     = "https://skills.example.org"
name    = "org-skills"
api_key = "your-secret-token"

Or manage them with the CLI:

# Register a server
oxo-call skill mcp add http://localhost:3000 --name local-skills

# Register an authenticated server
oxo-call skill mcp add https://skills.example.org \
    --name org-skills --api-key your-secret-token

# List registered servers
oxo-call skill mcp list

# Test connectivity
oxo-call skill mcp ping

# Remove a server
oxo-call skill mcp remove local-skills

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Building an MCP Skill Server

Any HTTP server that implements the three JSON-RPC methods above qualifies. Below is a minimal example in Python using the mcp SDK:

from mcp.server.fastmcp import FastMCP
from pathlib import Path

mcp = FastMCP("my-skills")
SKILLS_DIR = Path("./skills")   # directory of .md files

@mcp.resource("skill://{tool}")
def get_skill(tool: str) -> str:
    """Serve a skill Markdown file."""
    path = SKILLS_DIR / f"{tool}.md"
    if not path.exists():
        raise FileNotFoundError(f"No skill for '{tool}'")
    return path.read_text()

if __name__ == "__main__":
    mcp.run(transport="streamable-http", port=3000)

Skills served must follow the oxo-call skill format.

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Verification

After registering a server:

# Show all skills including MCP sources
oxo-call skill list

# Show a skill from an MCP server
oxo-call skill show mytool

# Ping all registered servers
oxo-call skill mcp ping

skill list shows MCP-sourced skills with a yellow mcp:<server-name> label. skill mcp ping reports each server's name, version, and skill count.

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Security Considerations

• api_key is stored in plain text in config.toml. Restrict file permissions (chmod 600 ~/.config/oxo-call/config.toml).
• Only http:// and https:// URLs are supported.
• Skill content from MCP servers is parsed and validated before use; invalid content is silently skipped.
• oxo-call does not execute any code returned by MCP servers. Skill content is only injected into LLM prompts.

See Security Considerations for the full security model.