Code Ocean MCP Server

Model Context Protocol (MCP) server for Code Ocean.

This MCP server provides tools to search and run capsules and pipelines, and manage data assets.

Table of Contents

• Prerequisites
• Installation
  • Visual Studio Code
  • Claude Desktop
  • Cline
  • Roo Code
  • Cursor
  • Windsurf

Prerequisites

1. Install uv from Astral or the GitHub README
2. Install Python 3.10 or newer using uv python install 3.10 (or a more recent version)
3. Generate a Code Ocean access token. Follow instructions in the Code Ocean user guide.

Installation

Visual Studio Code

Here's an example VS Code MCP server configuration:

{
    ...
    "mcp": {
        "inputs": [
            {
            "type": "promptString",
            "id": "codeocean-token",
            "description": "Code Ocean API Key", 
            "password": true
            }
        ],
        "servers": {
            "codeocean": {
                "type": "stdio",
                "command": "uvx",
                "args": ["codeocean-mcp-server"],
                "env": {
                    "CODEOCEAN_DOMAIN": "https://codeocean.acme.com",
                    "CODEOCEAN_TOKEN": "${input:codeocean-token}"
                }
            }
        },
    }
}

---

Claude Desktop

1. Open the claude_desktop_config.json file:

• macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
• Windows: %APPDATA%\Claude\claude_desktop_config.json

2. Under the top-level "mcpServers" object, add a "codeocean" entry. For a stdio transport (child-process) it looks like this:

{
  "mcpServers": {
    "codeocean": {
      "command": "uvx",
      "args": ["codeocean-mcp-server"],
      "env": {
        "CODEOCEAN_DOMAIN": "https://codeocean.acme.com",
        "CODEOCEAN_TOKEN": "<YOUR_API_KEY>"
      }
    }
  }
}

---

Cline

Cline stores all of its MCP settings in a JSON file called cline_mcp_settings.json. You can edit this either through the GUI (“Configure MCP Servers” in the MCP Servers pane) or by hand:

1. Open Cline and click the MCP Servers icon in the sidebar.
2. In the “Installed” tab, click Configure MCP Servers → this opens your cline_mcp_settings.json.
3. Add a "codeocean" server under the "mcpServers" key. For stdio transport:

{
  "mcpServers": {
    "codeocean": {
      "command": "uvx",
      "args": ["codeocean-mcp-server"],
      "env": {
        "CODEOCEAN_DOMAIN": "https://codeocean.acme.com",
        "CODEOCEAN_TOKEN": "<YOUR_API_KEY>"
      },
      "alwaysAllow": [],       // optional: list of tools to auto-approve
      "disabled": false        // ensure it’s enabled
    }
  }
}

4. Save the file. Cline will automatically detect and launch the new server, making your Code Ocean tools available in chat .

---

Roo Code

Roo Code’s MCP support is configured globally across all workspaces via a JSON settings file or through its dedicated MCP Settings UI

Via the MCP Settings UI:

1. Click the MCP icon in Roo Code’s sidebar. 
2. Select Edit MCP Settings (opens cline_mcp_settings.json). 
3. Under "mcpServers", add:

{
  "mcpServers": {
    "codeocean": {
      "command": "uvx",
      "args": ["codeocean-mcp-server"],
      "env": {
        "CODEOCEAN_DOMAIN": "https://codeocean.acme.com",
        "CODEOCEAN_TOKEN": "<YOUR_API_KEY>"
      }
    }
  }
}

4. Save and restart Roo Code; your Code Ocean tools will appear automatically.

Optional: Manually editing cline_mcp_settings.json

1. Locate cline_mcp_settings.json (in your home directory or workspace). 
2. Insert the same "codeocean" block under "mcpServers" as above.
3. Save and restart.

---

Cursor

Cursor stores MCP servers in a JSON file at either ~/.cursor/mcp.json (global) or {project}/.cursor/mcp.json (project-specific) .

1. Open .cursor/mcp.json (or create it if missing). 
2. Add under "mcpServers":

{
  "mcpServers": {
    "codeocean": {
      "command": "uvx",
      "args": ["codeocean-mcp-server"],
      "env": {
        "CODEOCEAN_DOMAIN": "https://codeocean.acme.com",
        "CODEOCEAN_TOKEN": "<YOUR_API_KEY>"
      }
    }
  }
}

3. Save the file. Cursor will automatically detect and launch the new server on next start. 

---

Windsurf

Windsurf (Cascade) uses mcp_config.json under ~/.codeium/windsurf/ (or via the Cascade → MCP Servers UI) .

1. Open your Windsurf Settings and navigate to Cascade → MCP Servers, then click View Raw Config to open mcp_config.json. 
2. Insert the following under "mcpServers":

{
  "mcpServers": {
    "codeocean": {
      "command": "uvx",
      "args": ["codeocean-mcp-server"],
      "env": {
        "CODEOCEAN_DOMAIN": "https://codeocean.acme.com",
        "CODEOCEAN_TOKEN": "<YOUR_API_KEY>"
      }
    }
  }
}

3. Save and restart Windsurf (or hit “Refresh” in the MCP panel).