MCP.Market

Galaxy MCP server

by galaxyproject·io.github.galaxyproject/galaxy-mcp·v1.3.0·39 stars
No reviews yet

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

A85/100grade A
Write a reviewInstall
What users say
No reviews yet
Be the first
Safety scan
A85/100

full report

Adoption
Growing

39 stars

Reviews

Write one

Nobody has reviewed Galaxy yet.

If you have run it, two minutes of your experience saves the next person an afternoon.

Galaxy tools (31, 6 write)

write = sends, deletes, buys or posts

Read from the package source without running it. The installed server may list more.

  • cancel_workflow_invocationwrite action

    Cancel a running workflow invocation

  • connect

    Connect to Galaxy server

  • create_historywrite action

    Create a new history to organize datasets and analyses.

  • download_dataset

    Download a dataset from Galaxy to the local filesystem or memory

  • get_collection_details

    Get detailed information about a dataset collection and its members

  • get_dataset_details

    Get detailed information about a specific dataset, optionally including a content preview

  • get_histories

    Get list of user's histories with optional pagination and filtering.

  • get_history_contents

    Get paginated contents (datasets and collections) from a specific history with ordering support

  • get_history_details

    Get history metadata and summary count ONLY - does not return actual datasets

  • get_invocations

    View workflow invocations in Galaxy

  • get_iwc_workflow_details

    Get comprehensive details about a specific IWC workflow before importing.

  • get_iwc_workflows

    Fetch all workflows from the IWC (Interactive Workflow Composer)

  • get_job_details

    Get detailed information about the job that created a specific dataset

  • get_server_info

    Get Galaxy server information including version, URL, and configuration details

  • get_tool_citations

    Get citation information for a specific tool

  • get_tool_details

    Get detailed information about a specific tool including its input parameters.

  • get_tool_panel

    Get the tool panel structure (toolbox)

  • get_tool_run_exampleswrite action

    Return the exact XML test definitions (inputs, outputs, assertions, required files) for a Galaxy tool so an LLM can study real, working run configurations.

  • get_user

    Get current user information

  • get_workflow_details

    Get detailed information about a specific workflow

  • import_workflow_from_iwc

    Import a workflow from IWC to the user's Galaxy instance

  • invoke_workflow

    Invoke (run) a workflow with specified inputs and parameters

  • list_history_ids

    Get a simplified list of history IDs and names for easy reference

  • list_workflows

    List workflows available in the Galaxy instance

  • recommend_iwc_workflows

    Semantic search for IWC workflows based on natural language description.

  • run_toolwrite action

    Run a Galaxy tool on datasets in a history.

  • search_iwc_workflows

    Search for workflows in the IWC (Intergalactic Workflow Commission) manifest.

  • search_tools_by_keywords

    Recommend Galaxy tools based on a list of keywords.

  • search_tools_by_name

    Search Galaxy tools whose name, ID, or description contains the given query (substring match).

  • upload_filewrite action

    Upload a local file to Galaxy for analysis.

  • upload_file_from_urlwrite action

    Upload a file from a URL to Galaxy

Public scan report

scanner v0.1.10 · 2026-09-28 · same rubric, same numbers if you re-run it

no findings
  • Code scan5 source files scanned25/25
  • –Live reliabilityno gateway calls yet and no remote to proben/a
  • –Tool poisoningtools not inspected (local package is not executed); not countedn/a
  • Auth qualitystatic API keys via environment variables6/15
  • Maintenancelast push 0 days ago15/15
  • Maintainer identityregistry namespace matches repository owner; GitHub account older than a year9/10
Overall 85/100. Components that don't apply are left out of the denominator. Any critical finding is an F.RubricAppeal a findingJSON

How Galaxy compares

Against every graded MCP server, from our own scans and uptime checks. Updated after each scan run.

Safety score
85/100
higher than 70% of 48,255 servers
Tools
31
the typical server has 7
Tools that change things
19%
typical: 0%. Fewer write tools means less an agent can break
GitHub stars
39
more than 93% of 28,688 servers

What its tools let an agent do: 23 read · 4 create · 1 change · 1 delete · 2 run or deploy

Install Galaxy in Claude Code, Cursor or VS Code

claude mcp add galaxy-mcp -- uvx galaxy-mcp
Add to Cursor

What the publisher says

From the Galaxy repository's README, as published. We do not edit it. Read it on GitHub

Galaxy MCP Server

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.

Project Overview

The repository holds two independent implementations of the same Galaxy operation set:

PyPI as galaxy-mcp. It reaches Galaxy through BioBlend and carries the larger tool surface. See the Python README.

  • mcp-server-galaxy-py/ -- the Python MCP server, published to

same operations two ways: a galaxy-cli command-line tool and a galaxy-mcp (Node) MCP server, both built on a shared framework-free core. See the galaxy-agent-tools README.

  • galaxy-agent-tools/ -- a TypeScript pnpm workspace offering the

The two are meant to stay in step: an operation keeps its name and its meaning across both. They are still separate codebases with separate release trains, though, so each README lists the operations that surface actually has -- read the one you are using.

Key Features

  • Galaxy Connection: Connect to any Galaxy instance with a URL and API key
  • OAuth Login (optional): Offer browser-based sign-in that exchanges credentials for temporary Galaxy API keys
  • Server Information: Retrieve comprehensive server details including version, configuration, and capabilities
  • Tools Management: Search the tool catalog, inspect a tool's inputs, and execute Galaxy tools
  • User-Defined Tools: Create, list, run, and deactivate unprivileged user-defined tools
  • Workflow Integration: Find and import workflows from the Intergalactic Workflow Commission (IWC), then invoke them and follow their invocations
  • History Operations: Manage Galaxy histories, datasets, and collections, and inspect the jobs behind them
  • File Management: Upload files to Galaxy from local storage or from a URL, and download results back
  • Pages: Read and write Galaxy-flavored markdown pages -- history-attached notebooks and standalone reports -- including their revision history
  • Verified Container Recommendation (optional): Resolve a real quay.io/biocontainers image for a set of conda packages instead of guessing one -- see Optional extras
  • Mock-based test suite: The default suite runs entirely against mocked Galaxy responses, so it needs no server; a separate suite against a live Galaxy is opt-in and skips when no credentials are configured

Optional extras

container-recommend

Enables the recommendbiocontainer tool, which resolves a verified quay.io/biocontainers image for a set of conda packages. Authoring a user-defined tool means naming a container, and a hallucinated image tag is the most common way a UDT passes validation and then dies at run time with manifest unknown. This wraps galaxy.toolutil.deps.mulled.recommend -- the same resolver Galaxy's own custom-tool agent uses (added in Galaxy 26.1, galaxyproject/galaxy#22981) -- so the image is checked against quay.io rather than invented.

It is an extra rather than a hard dependency because galaxy-tool-util pulls in lxml and conda-package-streaming, and every other tool on this server works without it. The tool is only registered when the extra is installed, so a stock install simply doesn't advertise it.

uvx --from 'galaxy-mcp[container-recommend]' galaxy-mcp
# or, for a local checkout:
cd mcp-server-galaxy-py && uv sync --extra container-recommend

The same resolver is also available as a standalone CLI once installed: mulled-recommend samtools=1.17.

code-mode

Shortened. The full README is on GitHub.

Nothing above is checked by us. What we check is on the safety report.

Galaxy: common questions

Is Galaxy MCP server safe?
Yes, by our scan: it is graded A (85/100). Read the Galaxy safety report
How do I install Galaxy?
It runs on your machine. Copy the Claude Code, Cursor, VS Code or Claude Desktop config from the install section.
Does Galaxy need an API key?
Yes. The registry entry asks for GALAXY_API_KEY.
Is Galaxy maintained?
The last commit was 37 days ago (2026-09-28). The latest release is v1.3.0.
How does Galaxy compare with other MCP servers?
safety score 85/100 (higher than 70% of 48,255 servers); tools 31 (the typical server has 7); tools that change things 19% (typical: 0%. Fewer write tools means less an agent can break). Full comparison.