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Galaxy MCP Server

by galaxyproject Your server? Claim it
local only

Galaxy MCP runs on your own machine — the client starts it, so there is no endpoint to ping. 302 installs a week from pypi. Last commit 17 Sep 2026.

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

Installs per day peak 321 · avg 45 · +103% w/w
a month agotoday
302
Installs / week
pypi · galaxy-mcp
38
Stars
12 open issues
17 Sep 2026
Last commit
0 releases in 90 days
MIT
License
Python

What the code does

We read the source, 22 h ago · rules 3dff92dd89df

Capabilities

What this server is able to do. For an MCP server this is often the job itself — a terminal server runs commands because that is what it is for. Listed so you know what you are plugging in, not as an accusation.

File ships in the package but is absent from the source [пакет] src/galaxy_mcp/__init__.py:1, [пакет] src/galaxy_mcp/__main__.py:1, [пакет] src/galaxy_mcp/auth.py:1 и ещё 4
этот файл ставится пользователю, но в репозитории его нет

Is this your server and something here is wrong? Tell us — corrections are free and do not require a plan.

This code can reach further than it looks

We found places where it runs commands, builds paths or queries from values it is given. None of that is a flaw by itself — it becomes one when the code changes, and code changes quietly between releases. We re-read it on every one.

Three servers free · no card

Connect this server

This server runs on your own machine — install it with the package manager and the client starts it for you. Package name taken from the official registry entry.

run in your terminal
claude mcp add galaxy-mcp -- uvx galaxy-mcp
~/Library/Application Support/Claude/claude_desktop_config.json
{
  "mcpServers": {
    "galaxy-mcp": {
      "args": [
        "galaxy-mcp"
      ],
      "command": "uvx"
    }
  }
}
~/.codex/config.toml
[mcp_servers.galaxy-mcp]
command = "uvx"
args = ["galaxy-mcp"]
.cursor/mcp.json
{
  "mcpServers": {
    "galaxy-mcp": {
      "args": [
        "galaxy-mcp"
      ],
      "command": "uvx"
    }
  }
}
.vscode/mcp.json
{
  "mcpServers": {
    "galaxy-mcp": {
      "args": [
        "galaxy-mcp"
      ],
      "command": "uvx"
    }
  }
}

This one needs environment variables set before it will start: GALAXY_URL (URL of the Galaxy instance to connect to (e.g., https://usegalaxy.org)), GALAXY_API_KEY (API key for authenticating with the Galaxy instance). The author declared them in the registry entry; get the values from the project itself.

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answering

Galaxy MCP — questions

Answers built from our own checks of this server.

Why is there no uptime for Galaxy MCP?
Galaxy MCP runs on your own machine over stdio — there is no network address to reach, so uptime cannot be measured for it by anyone. What can be measured is adoption: the pypi package galaxy-mcp was installed 302 times last week.
How do I connect Galaxy MCP?
Copy the ready config from this page — we generate it for Claude Code, Claude Desktop, Codex, Cursor and VS Code, each with the file path that client actually reads. It runs locally, so the command pulls galaxy-mcp straight from pypi; nothing to host, nothing to sign up for.
How many people use Galaxy MCP?
The pypi package galaxy-mcp was installed 302 times in the last week. Week over week that is +103%. We show installs rather than GitHub stars on purpose: a star is a bookmark, an install is someone actually running it.
Is Galaxy MCP open source?
Yes — it is published under the MIT licence, written in Python, 38 stars on GitHub and 12 open issues. The source link is on this page, so you can read exactly what it does with your data before you connect it.