Best for
- Bioinformatics researchers who want AI assistants to operate the Galaxy platform
- Galaxy instance administrators and regular Galaxy users
- Teams automating analysis workflows
G
Galaxy MCP Server
Official
MCP server for the Galaxy bioinformatics platform
GitHub source repository ↗
61FMRS · C
An officially maintained, MIT-licensed MCP server from the Galaxy Project built on BioBlend. It provides Galaxy connection, tool search/execution, workflow and history management, file upload, stdio and streamable-http transports, optional OAuth login, and a full test suite. Best suited for Galaxy users bringing the platform into AI assistants, provided they have Galaxy access credentials.
Galaxy MCP Server is an open-source (MIT) MCP server maintained by the Galaxy Project. It lets AI assistants connect to any Galaxy instance to search and execute tools, manage workflows and histories, upload files, and optionally authenticate via browser-based OAuth. The Python implementation is built on BioBlend, and the repository also ships a TypeScript workspace (galaxy-agent-tools) offering a galaxy-cli tool and a Node MCP server kept in lockstep.
Setup
Run via uvx (uvx galaxy-mcp, stdio by default), or pip install galaxy-mcp and run galaxy-mcp, or use the Docker image galaxyproject/galaxy-mcp. Set required environment variables GALAXY_URL (Galaxy instance URL) and GALAXY_API_KEY (API key). For HTTP: uvx galaxy-mcp --transport streamable-http --host 0.0.0.0 --port 8000. For Claude Desktop, add a galaxy-mcp entry to claude_desktop_config..
claude_desktop_config.json
{"mcpServers":{"galaxy-mcp":{"command":"uvx","args":["galaxy-mcp"],"env":{"GALAXY_URL":"https://usegalaxy.org","GALAXY_API_KEY":"SECRETS"}}}}
Fit and risk
Not for
- Users not on the Galaxy platform
- Environments without a Galaxy URL and API key
- General-purpose bioinformatics outside Galaxy
Required permissions
- Requires the target Galaxy instance URL (GALAXY_URL, required)
- Requires a Galaxy API key (GALAXY_API_KEY, required and secret; may be omitted when using OAuth)
- OAuth mode requires a session secret (GALAXY_MCP_SESSION_SECRET) and public URL (GALAXY_MCP_PUBLIC_URL)
Risks and side effects
- The API key is a sensitive credential; leakage grants others access to your Galaxy account and analyses
- Tools and workflows executed by the AI consume Galaxy compute resources
- Remote HTTP deployment exposes a network port and requires careful OAuth and session-secret configuration
Troubleshooting
- Verify GALAXY_URL and GALAXY_API_KEY are set correctly and point at the intended Galaxy instance
- Check the developer menu in Claude Desktop shows galaxy-mcp running; restart Claude Desktop if needed
- If env config is missing, provide connection details in chat (e.g., your Galaxy API key)
- For OAuth login, ensure GALAXY_MCP_PUBLIC_URL and GALAXY_MCP_SESSION_SECRET are configured
Use cases
Search and execute Galaxy tools via conversation
Import and manage workflows from the IWC catalog
Manage Galaxy histories and datasets
Upload local files to Galaxy
Share one server across users with per-session credential isolation
Supported clients
Claude DesktopFull support