Koskamo

Galaxy MCP

An MCP server enabling AI assistants to connect to Galaxy bioinformatics instances, search and execute tools, manage workflows, handle histories, and upload/download files via BioBlend or native implementations.

Package and access

Local package with source-attributed installation metadata. Koskamo does not execute packages during review.

Galaxy MCP logo, by Galaxy ProjectCommunity listingLocal stdioSource reviewed; not executedPublished by Galaxy Project
You need:Connect to any Galaxy instance with a URL and API key
Vendor documentation

What you can do with it

  • Connect to Galaxy instances and execute bioinformatics tools
  • Manage workflows and history operations
  • Upload files and download results
  • Search tool catalog and inspect inputs

Source and maintenance

Community listingRegistry 1.3.0
mcp-registry: io.github.galaxyproject/galaxy-mcp@1.3.0Source repository
Maintenance checked

Packages and installation

Source-provided package data. Koskamo has not executed or live-probed this package.

galaxy-mcp 1.3.0

pypi
galaxy-mcp package definition
{
  "version": "1.3.0",
  "transport": "stdio",
  "identifier": "galaxy-mcp",
  "registryType": "pypi",
  "environmentVariables": [
    {
      "name": "GALAXY_URL",
      "format": "string",
      "isRequired": true,
      "description": "URL of the Galaxy instance to connect to (e.g., https://usegalaxy.org)"
    },
    {
      "name": "GALAXY_API_KEY",
      "format": "string",
      "isRequired": true,
      "description": "API key for authenticating with the Galaxy instance"
    }
  ]
}

Tools

Reported by the attributed source; not independently observed by Koskamo.

No tool definitions available.

Connect from your client

Each snippet configures the same source-provided package; replace placeholders before use.

This server is operated by the named third party. Listing and endpoint checks are not an endorsement or a security audit. Review the operator's permissions, terms, and data handling before connecting. How listings are checked and corrected.

Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.
Cursor configuration
{
  "mcpServers": {
    "galaxy-mcp": {
      "command": "uvx",
      "args": [
        "galaxy-mcp==1.3.0"
      ],
      "env": {
        "GALAXY_URL": "<YOUR_GALAXY_URL>",
        "GALAXY_API_KEY": "<YOUR_GALAXY_API_KEY>"
      }
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.
Cline configuration
{
  "mcpServers": {
    "galaxy-mcp": {
      "command": "uvx",
      "args": [
        "galaxy-mcp==1.3.0"
      ],
      "env": {
        "GALAXY_URL": "<YOUR_GALAXY_URL>",
        "GALAXY_API_KEY": "<YOUR_GALAXY_API_KEY>"
      }
    }
  }
}

VS Code

Merge this local stdio configuration, replace every placeholder environment value, and restart VS Code. Koskamo has not executed this package.
VS Code configuration
{
  "servers": {
    "galaxy-mcp": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "galaxy-mcp==1.3.0"
      ],
      "env": {
        "GALAXY_URL": "<YOUR_GALAXY_URL>",
        "GALAXY_API_KEY": "<YOUR_GALAXY_API_KEY>"
      }
    }
  }
}

Claude Desktop

Merge this local stdio configuration, replace every placeholder environment value, and restart Claude Desktop. Koskamo has not executed this package.
Claude Desktop configuration
{
  "mcpServers": {
    "galaxy-mcp": {
      "command": "uvx",
      "args": [
        "galaxy-mcp==1.3.0"
      ],
      "env": {
        "GALAXY_URL": "<YOUR_GALAXY_URL>",
        "GALAXY_API_KEY": "<YOUR_GALAXY_API_KEY>"
      }
    }
  }
}

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