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How to add gget-mcp to Windsurf

Bioinformatics MCP server wrapping the gget toolkit for gene, sequence, structure, and enrichment queries. Paste the config into ~/.codeium/windsurf/mcp_config.json and restart Windsurf.

Last updated June 14, 2026 · 29★ · stdio · no auth

Windsurf config for gget-mcp

uvx --from gget-mcp@latest stdio
{
  "mcpServers": {
    "gget-mcp": {
      "command": "uvx",
      "args": [
        "--from",
        "gget-mcp@latest",
        "stdio"
      ]
    }
  }
}

Requires `uv` (the Python package runner). Install it from https://docs.astral.sh/uv/ if `uvx` is not found.

Setup steps

  1. 1Open Windsurf → Cascade → the hammer/MCP icon → Configure (or edit ~/.codeium/windsurf/mcp_config.json).
  2. 2Paste the gget-mcp config below.
  3. 3Fill in placeholder secrets, then save.
  4. 4Click Refresh in the MCP panel.
  5. 5gget-mcp's tools become available to Cascade.

Before you start

  • uv / uvx (or Python 3.10+) to run the server
  • Stable internet connection (gget tools query external genomic databases and web services)
  • An MCP-compatible client such as Claude Desktop, Cursor, or Windsurf

What gget-mcp can do in Windsurf

gget_search

Find Ensembl IDs associated with search terms.

gget_info

Fetch detailed information for Ensembl IDs.

gget_seq

Retrieve nucleotide or amino acid sequences (supports translate=True for protein).

gget_ref

Get reference genome information from Ensembl.

gget_blast

BLAST nucleotide or amino acid sequences to identify their origin.

gget_blat

Find the genomic locations of sequences.

gget_muscle

Align multiple sequences (MUSCLE) and identify conserved regions.

gget_archs4

Get gene expression data from ARCHS4 across tissues.

Security

No API key is required for the core server, but many gget tools query external web services and databases that may be rate-limited or temporarily unavailable. The optional LLM-based 'judge' tests require API keys (e.g. GEMINI_API_KEY) and may incur costs, but these are for development only and are not needed to run the server.

gget-mcp + Windsurf FAQ

Where is the Windsurf config file?

Windsurf reads MCP servers from ~/.codeium/windsurf/mcp_config.json. Paste the gget-mcp config there under the "mcpServers" key and restart the client.

Is gget-mcp safe to use with Windsurf?

No API key is required for the core server, but many gget tools query external web services and databases that may be rate-limited or temporarily unavailable. The optional LLM-based 'judge' tests require API keys (e.g. GEMINI_API_KEY) and may incur costs, but these are for development only and are not needed to run the server.

Do I need an API key?

No. The core server requires no API key. Many tools query external public databases, so an internet connection is needed. Only the optional development 'judge' tests require LLM API keys.

Which transport modes are supported?

STDIO (recommended for MCP clients and for saving large outputs to disk), HTTP (default port 3002, endpoint /mcp, docs at /docs), and SSE.

Is this an official gget tool?

No. gget-mcp is built by the Longevity Genie project and wraps the gget library from pachterlab; it is a community/third-party MCP wrapper.

View repo Full gget-mcp page