INDIVIDUAL MCP TOOL

find_path

Finds the shortest pipeline path between two skills, annotated with data flow (what data types pass between each step), paper counts, and evidence.

pipette.bionone authenticationAvailability not checked

LIVE ENDPOINT

https://skillgraph.pipette.bio/mcp

No auth detected

Connect to this endpoint to inspect the live schema for find_path and invoke it with your own arguments.

{}

Inferred read-only · medium confidence · heuristic, not a guarantee.

No write-capable action terms were found; this is not proof that invocation has no side effects.

CONNECT WITH APPROVAL

Review this server and its permissions before adding it. Secret placeholders must be set locally.

Codex

~/.codex/config.toml

[mcp_servers.skillgraph]
url = "https://skillgraph.pipette.bio/mcp"
enabled = true

Claude Code

.mcp.json

{
  "mcpServers": {
    "skillgraph": {
      "type": "http",
      "url": "https://skillgraph.pipette.bio/mcp"
    }
  }
}

Claude Desktop

Settings → Connectors → Add custom connector

Name: skillgraph
Remote MCP URL: https://skillgraph.pipette.bio/mcp

Add this remote URL as a custom connector in Claude Desktop. Availability depends on the user plan and workspace policy.

Cursor

.cursor/mcp.json

{
  "mcpServers": {
    "skillgraph": {
      "url": "https://skillgraph.pipette.bio/mcp"
    }
  }
}

Visual Studio Code

.vscode/mcp.json

Add to Visual Studio Code

{
  "servers": {
    "skillgraph": {
      "type": "http",
      "url": "https://skillgraph.pipette.bio/mcp"
    }
  }
}

Generic MCP

Client-specific MCP configuration

{
  "name": "skillgraph",
  "transport": "streamable-http",
  "url": "https://skillgraph.pipette.bio/mcp"
}

MCP Inspector

Run the official MCP Inspector locally and enter the indexed Streamable HTTP endpoint.

get_skill — Returns full SKILL.md documentation for a bioinformatics skill, plus its overview, tools, I/O data types, and upstream/downstream connections.
list_skills — Lists all available bioinformatics skills in the graph, optionally filtered by a domain keyword (e.g., 'rna-seq', 'variant', 'drug').
search_skills — Keyword search across skill IDs, trigger keywords, and tool names.
get_transitions — Returns upstream and/or downstream skills connected to a given skill in the pipeline graph, with edge evidence (paper counts, data types, ground truth status).
get_graph_stats — Returns summary statistics about the SkillGraph knowledge graph: total skills, edges, literature vs inferred edges, and a breakdown of skills by domain (single-cell, variant analysis, drug discovery, etc.).