# galaxy-mcp

Links AI clients with the Galaxy bioinformatics platform. Run analysis tools, manage histories, and track complex scientific pipelines right from the chat.

- MCP server · `type=mcp` · Claude Code, Codex, Cursor, GitHub Copilot, Windsurf (Devin Desktop), Cline, Zed, Gemini CLI · ★ 39
- Author: galaxyproject
- License: MIT · policy=link-only · description only; the file stays with the author
- Source: https://github.com/galaxyproject/galaxy-mcp
- Updated: 2026-10-23
- HTML: https://affpapa.org/en/nevibecode/mcp/galaxy-mcp

## What it does

This server exposes Galaxy bioinformatics instances to MCP clients via standard I/O or HTTP streaming. It provides tools to search the platform catalog, inspect parameter schemas, and execute computational jobs. Clients can also manage histories, handle dataset collections, and import validated workflows from the Intergalactic Workflow Commission.

The environment requires an active `GALAXY_URL` alongside a valid `GALAXY_API_KEY` for authentication. Without these credentials, requests to schedule jobs or fetch data will fail immediately. An optional `code-mode` flag collapses the catalog into three meta-tools to preserve context windows, while the `container-recommend` extra verifies `quay.io/biocontainers` images for custom tool definitions.

## Requirements
- Needs: Python and uv (commands run via uvx)
- Environment variables: `GALAXY_URL`, `GALAXY_API_KEY` — keys and tokens: ask the human for the values, never commit them or put them in shared files.

## Install

### Claude Code (native platform)

**Platform CLI**
```bash
claude mcp add galaxy-mcp -e GALAXY_URL=<GALAXY_URL> -e GALAXY_API_KEY=<GALAXY_API_KEY> -- uvx galaxy-mcp
```
Replace <…> with your own values. uvx runs the command named after the package; if the README names another one, use uvx --from galaxy-mcp <command>

### Codex

**Platform CLI**
```bash
codex mcp add galaxy-mcp --env GALAXY_URL=<GALAXY_URL> --env GALAXY_API_KEY=<GALAXY_API_KEY> -- uvx galaxy-mcp
```
Replace <…> with your own values. uvx runs the command named after the package; if the README names another one, use uvx --from galaxy-mcp <command>

### Cursor

**Config file**
File `.cursor/mcp.json`:
```json
{
    "mcpServers": {
        "galaxy-mcp": {
            "command": "uvx",
            "args": [
                "galaxy-mcp"
            ],
            "env": {
                "GALAXY_URL": "<GALAXY_URL>",
                "GALAXY_API_KEY": "<GALAXY_API_KEY>"
            }
        }
    }
}
```
Replace <…> with your own values. uvx runs the command named after the package; if the README names another one, use uvx --from galaxy-mcp <command>

### GitHub Copilot

**Config file**
File `.vscode/mcp.json`:
```json
{
    "servers": {
        "galaxy-mcp": {
            "type": "stdio",
            "command": "uvx",
            "args": [
                "galaxy-mcp"
            ],
            "env": {
                "GALAXY_URL": "<GALAXY_URL>",
                "GALAXY_API_KEY": "<GALAXY_API_KEY>"
            }
        }
    }
}
```
Replace <…> with your own values. uvx runs the command named after the package; if the README names another one, use uvx --from galaxy-mcp <command>

### Gemini CLI

**Platform CLI**
```bash
gemini mcp add -e GALAXY_URL=<GALAXY_URL> -e GALAXY_API_KEY=<GALAXY_API_KEY> galaxy-mcp uvx galaxy-mcp
```
Replace <…> with your own values. uvx runs the command named after the package; if the README names another one, use uvx --from galaxy-mcp <command>

## When to use it
- Trigger Galaxy analysis jobs and monitor job progress through chat
- Import and execute pipelines from the Intergalactic Workflow Commission
- Upload biological sequence files to histories and retrieve generated outputs
- Draft Galaxy markdown pages with embedded datasets and revisions

## Example prompts
- Inspect the input parameters for the fastqc tool in my Galaxy instance
- Import the latest RNA-seq workflow from IWC and display its steps
- Create a new history and upload my sequence file from this local path

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