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MCP Server

io.github.galaxyproject/galaxy-mcp MCP Server

io.github.galaxyproject/galaxy-mcp

RepositoryRegistry

What is the io.github.galaxyproject/galaxy-mcp MCP server?

MCP server for Galaxy bioinformatics platform - connect, execute tools, and manage workflows

How to install io.github.galaxyproject/galaxy-mcp

Copy-paste configuration for popular MCP clients.

transport: stdio
Config generated by PluginBench — verify against the source before use.
Environment / auth
  • GALAXY_URL
    required

    URL of the Galaxy instance to connect to (e.g., https://usegalaxy.org)

  • GALAXY_API_KEY
    required
    secret

    API key for authenticating with the Galaxy instance

Claude Desktop
~/Library/Application Support/Claude/claude_desktop_config.json
{
  "mcpServers": {
    "galaxy-mcp": {
      "command": "uvx",
      "args": [
        "galaxy-mcp"
      ],
      "env": {
        "GALAXY_URL": "<YOUR_GALAXY_URL>",
        "GALAXY_API_KEY": "<YOUR_GALAXY_API_KEY>"
      }
    }
  }
}
Cursor
~/.cursor/mcp.json
{
  "mcpServers": {
    "galaxy-mcp": {
      "command": "uvx",
      "args": [
        "galaxy-mcp"
      ],
      "env": {
        "GALAXY_URL": "<YOUR_GALAXY_URL>",
        "GALAXY_API_KEY": "<YOUR_GALAXY_API_KEY>"
      }
    }
  }
}
Windsurf
~/.codeium/windsurf/mcp_config.json
{
  "mcpServers": {
    "galaxy-mcp": {
      "command": "uvx",
      "args": [
        "galaxy-mcp"
      ],
      "env": {
        "GALAXY_URL": "<YOUR_GALAXY_URL>",
        "GALAXY_API_KEY": "<YOUR_GALAXY_API_KEY>"
      }
    }
  }
}
VS Code
.vscode/mcp.json
{
  "servers": {
    "galaxy-mcp": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "galaxy-mcp"
      ],
      "env": {
        "GALAXY_URL": "<YOUR_GALAXY_URL>",
        "GALAXY_API_KEY": "<YOUR_GALAXY_API_KEY>"
      }
    }
  }
}
Claude Code
claude mcp add galaxy-mcp --env GALAXY_URL=<YOUR_GALAXY_URL> --env GALAXY_API_KEY=<YOUR_GALAXY_API_KEY> -- uvx galaxy-mcp

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