MCP server

galaxy-mcp

Repository:: github.com/galaxyproject/galaxy-mcp
Stars:: 39
Last push:: 2026-10-27
License:: MIT

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

Good fit for

One-command install
Runs fully local
MIT license

Facts

Category: Research and education
Pricing: Unknown
Authentication: API key
Transport: stdio
Hosting: Local
Maker: Unknown
Access: Unknown
Language: TypeScript, Python
Install method: uvx
Operating system: Unknown
Client: Unknown
License: Permissive
Maintenance: Active

Install

claude mcp add --env 'GALAXY_URL=<YOUR_VALUE>' --env 'GALAXY_API_KEY=<YOUR_VALUE>' --transport stdio galaxy-mcp -- uvx galaxy-mcp

Paste into claude_desktop_config.json

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

Paste into ~/.cursor/mcp.json

{
  "mcpServers": {
    "galaxy-mcp": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "galaxy-mcp"
      ],
      "env": {
        "GALAXY_URL": "<YOUR_VALUE>",
        "GALAXY_API_KEY": "<YOUR_VALUE>"
      }
    }
  }
}

Paste into .vscode/mcp.json

{
  "servers": {
    "galaxy-mcp": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "galaxy-mcp"
      ],
      "env": {
        "GALAXY_URL": "<YOUR_VALUE>",
        "GALAXY_API_KEY": "<YOUR_VALUE>"
      }
    }
  }
}

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

[mcp_servers.galaxy-mcp]
command = "uvx"
args = ["galaxy-mcp"]
env = { GALAXY_URL = "<YOUR_VALUE>", GALAXY_API_KEY = "<YOUR_VALUE>" }

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

Env vars and secrets

GALAXY_URLEnv var
URL of the Galaxy instance to connect to (e.g., https://usegalaxy.org)
GALAXY_API_KEYEnv varSecret
API key for authenticating with the Galaxy instance

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Score: 72

Popularity: 46
Maintenance: 100
Trust: 73
Completeness: 90
Community: 50

Formula version 1

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