Galaxy MCP Server: Install & Setup

Install Galaxy in Claude Code

Claude Code

claude mcp add galaxy -e GALAXY_URL=... -e GALAXY_API_KEY=... -- uvx galaxy-mcp

mcp.json (Claude Desktop, Cursor, VS Code, Windsurf)

{
  "mcpServers": {
    "galaxy": {
      "command": "uvx",
      "args": [
        "galaxy-mcp"
      ],
      "env": {
        "GALAXY_URL": "...",
        "GALAXY_API_KEY": "..."
      }
    }
  }
}

Replace each ... with your own value.

Frequently asked questions

What does the Galaxy MCP server do?

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

Is the Galaxy MCP server free?

The server is free, but you will likely need an account. The server itself is free, but it connects to a service that needs an account or API key, which may have paid tiers. Check the provider for current pricing.

Does Galaxy run locally or remotely?

Local. Runs on your machine (stdio). You install it with npx, uvx, Docker or from source.

How do I add Galaxy to Claude Code?

Run: claude mcp add galaxy -e GALAXY_URL=... -e GALAXY_API_KEY=... -- uvx galaxy-mcp

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