10x Genomics MCP Server for Claude Desktop

10x Genomics Cloud MCP server for Claude Desktop.

Deploy to Claude Desktop

1. Build (see Installation section below) or download .mcpb package from Releases.
2. Open Claude Desktop
3. Go to Settings > Extensions > Browse
4. Install the package
5. Configure your access token

Installation

Prerequisites

• Node.js 18+ (comes with Claude Desktop)
• Access to 10x Genomics Cloud platform
• Valid 10x Genomics access token

Development Setup

# 1. Install dependencies
npm install

# 2. Build TypeScript
npm run build

# 3. Run tests
npm test

# 4. Download TXG Binaries (or manually create them in package/bin/<darwin|linux|windows>):
npm run download-bin

# 5. Create MCP bundle
npm run pack

# 6. Deploy
 # Open Claude Desktop
 # Go to Settings > Extensions > Browse
 # Install .mcpb file

# 7. Query server capabilities and update reference documentation
# note: this is not needed for functionality, just make sure to run it before submitting a PR (makes it easier to review changes to the mcp APIs)
npm run generate-capabilities

# 8. For complete release build (clean + build + test + capabilities + pack):
npm run release

Access Token Management

The server requires a 10x Genomics access token. There are several ways to provide it:

1. Pass as argument (saved for future use):

   npm run start YOUR_ACCESS_TOKEN

2. Use saved token (from credentials.txt):

   npm run start

The token is automatically saved to credentials.txt (gitignored) when provided as an argument.

Project Structure

  txg-mcp/
  ├── src/                   # TypeScript source code for MCP server
  ├── tests/                 # Test files
  ├── build/                 # Compiled JavaScript and binaries (content of the mcpb file)
  │   ├── server/            # Compiled server code
  │   ├── bin/               # Platform-specific TXG binaries
  │   └── node_modules/      # mcpb node dependencies
  ├── assets/                # Static assets
  ├── reference/             # Reference capabilities
  ├── scripts/               # Build and utility scripts
  ├── package.json           # NPM package configuration
  ├── manifest.json          # Claude Desktop extension manifest
  ├── tasks.sh               # Task for build, package, test, ..etc script
  ├── txg-node.mcpb          # MCP bundle file (output of npm run pack) - not this can be renamed to .zip to examine it's content
  └── credentials.txt        # Your access token (gitignored)

Features

• 25+ Tools for managing Cell Ranger analyses, projects, files, and references
• Smart parameter confirmation via MCP prompts
• Async/await throughout for non-blocking operations
• Zod validation for type-safe parameter handling
• Structured error handling with detailed responses

How It Works

1. Claude Desktop starts the Node.js server via node server/index.js
2. Server communicates via stdio using MCP protocol (JSON-RPC 2.0)
3. Tools translate Claude's requests to TXG CLI commands
4. TXG CLI talk to Cloud Analysis APIs
5. Responses are formatted and returned to Claude

Claude Desktop Extension Documentation

• Documentation: Anthropic Desktop Extensions Documentation
• MCP Protocol: Model Context Protocol Specification