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Galaxy Mcp

io.github.galaxyproject/galaxy-mcp · v1.3.0

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

Connect Runs on your machine

Terminal
claude mcp add galaxy-mcp -e GALAXY_URL=<GALAXY_URL> -e GALAXY_API_KEY=<GALAXY_API_KEY> -- uvx galaxy-mcp==1.3.0
claude_desktop_config.json
{
  "mcpServers": {
    "galaxy-mcp": {
      "command": "uvx",
      "args": [
        "galaxy-mcp==1.3.0"
      ],
      "env": {
        "GALAXY_URL": "<GALAXY_URL>",
        "GALAXY_API_KEY": "<GALAXY_API_KEY>"
      }
    }
  }
}
~/.cursor/mcp.json
{
  "mcpServers": {
    "galaxy-mcp": {
      "command": "uvx",
      "args": [
        "galaxy-mcp==1.3.0"
      ],
      "env": {
        "GALAXY_URL": "<GALAXY_URL>",
        "GALAXY_API_KEY": "<GALAXY_API_KEY>"
      }
    }
  }
}
.vscode/mcp.json
{
  "servers": {
    "galaxy-mcp": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "galaxy-mcp==1.3.0"
      ],
      "env": {
        "GALAXY_URL": "<GALAXY_URL>",
        "GALAXY_API_KEY": "<GALAXY_API_KEY>"
      }
    }
  }
}

Replace the values in angle brackets with your own. Keys stay on your machine; we never see them.

Tools

This server runs locally, so its tools are listed by your MCP client once it starts.

Environment variables

NameDescription
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

Details

Package[email protected] (PYPI, stdio)
First published29 Jan 2026
Last updated29 Jan 2026
Registry nameio.github.galaxyproject/galaxy-mcp

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