Galaxy MCP

This project provides a Model Context Protocol (MCP) server for interacting with the Galaxy bioinformatics platform. It enables AI assistants and other clients to connect to Galaxy instances, search and execute tools, manage workflows, and access other features of the Galaxy ecosystem. It runs locally over stdio via the published package.

People connecting automation tools to Claude, Cursor, VS Code, or another MCP client. The project is written in Python.

VERIFIED ACTIVE

LAST COMMIT 2026-08-12 · ★ 38 · #63 OF 194 MAINTAINED AUTOMATION · VERIFIED 2026-08-25

MIT · Python servers · how we verify → /methodology

01 · Install Galaxy MCP

before you install - you'll need

Set GALAXY_URL, GALAXY_API_KEY, GALAXY_MCP_PUBLIC_URL, GALAXY_MCP_SESSION_SECRET, GALAXY_MCP_TRANSPORT before connecting.

Claude Code

claude mcp add galaxyproject-galaxy-mcp -- uvx galaxy-mcp

Claude Desktop / Cursor / VS Code - add to config

{
  "mcpServers": {
    "galaxyproject-galaxy-mcp": {
      "command": "uvx",
      "args": [
        "galaxy-mcp"
      ]
    }
  }
}

Same JSON for Cursor. For VS Code, rename the top-level key from `mcpServers` to `servers`.

Using another client? Same JSON, different key

Claude Desktop · mcpServers

Cursor · mcpServers

VS Code · servers

Windsurf · mcpServers

Zed · context_servers

Cline · mcpServers

Roo Code · mcpServers

Continue · mcpServers

LibreChat · mcpServers

Gemini CLI · mcpServers

Codex CLI · mcp_servers

Full setup guides: every client.

02 · Evidence

Security posture

What to check before giving this server access to your agent - from the registry, GitHub, and our own probes. We don't score safety; we show what's verifiable.

runs as local process (stdio) - runs on your machine with your user's permissions

license MIT - declared in the repository

pypi package galaxy-mcp - check the name against the project README before installing (PyPI has no namespace ownership)

registry namespace io.github.galaxyproject is GitHub-verified and matches the repo owner

03 · What Galaxy MCP can do

Prose above is summarized from the project's README and registry record - no invented capabilities.

Latest releases

v1.9.0 · 2026-06-20

Changes · Add Galaxy Pages (notebook/report) tools @dannon (#84) · Add a shared agent-operations core (galaxy-ops) for MCP, CLI, and code-mode @dannon (#61) · Add 23 ops to galaxy-ops for full mcp-server-galaxy-py…

v1.8.0 · 2026-06-12

Changes · Run user-defined tools through POST /api/tools (restores 26.0 compatibility) @dannon (#70) · Add OAuth token-lifecycle tests (auth.py 29% -> 58%) @dannon (#67) · Bump mypy to 1.20 and fix client_id…

v1.7.0 · 2026-06-10

Changes · Add workflow input templates + invoke-time datatype validation @dannon (#55) · Add a run guide + resolved parameter options to get_workflow_input_template @dannon (#60) · Fix style=run resolving the wrong…

04 · Who maintains Galaxy MCP

galaxy-mcp is maintained by galaxyproject. It's the only MCP server we track from this author; the repo dates to Mar 2025.

05 · Facts

repository: github.com/galaxyproject/galaxy-mcp
category: automation - ranked #63 of 194 actively-maintained automation servers as of 2026-08-25.
release cadence: 5 releases in the last 90 days (latest 2026-06-20)
registry: io.github.galaxyproject/galaxy-mcp (active, first published 2026-01-29)
packages: pypi:galaxy-mcp

06 · Galaxy MCP FAQ

What is Galaxy MCP?

Is Galaxy MCP still maintained?

Yes - as of 2026-08-25, its last commit was 2026-08-12 and it shipped 5 releases in the last 90 days. We re-verify nightly.

How do I install Galaxy MCP?

Run `uvx galaxy-mcp`. The README documents 5 environment variables (GALAXY_URL, GALAXY_API_KEY, GALAXY_MCP_PUBLIC_URL…) to set first. Set GALAXY_URL, GALAXY_API_KEY, GALAXY_MCP_PUBLIC_URL, GALAXY_MCP_SESSION_SECRET, GALAXY_MCP_TRANSPORT before connecting. You can also paste the ready-made client config above.

Does Galaxy MCP run locally?

Yes - it's a stdio server: it runs on your machine (via uvx) with your user's permissions. Your data stays local unless the server itself calls external APIs.

07 · Alternatives to Galaxy MCP

Alternatives to Galaxy MCP

Maintained automation servers if Galaxy MCP isn't the fit.

More automation MCP servers · Glif · Goodeye · Desktop Touch MCP · n8n Pro MCP

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