gget-mcp

This server implements the Model Context Protocol (MCP) for gget, providing a standardized interface for accessing powerful bioinformatics tools and databases. MCP enables AI assistants and agents to perform complex genomics queries through structured interfaces.

The gget bioinformatics toolkit provides efficient querying of genomic databases and includes functions for:

- Gene and sequence information retrieval
- BLAST and sequence alignment
- Protein structure prediction
- Gene expression analysis
- Functional enrichment analysis
- And much more!

👤 User:"Analyze the TP53 gene - find its details and protein sequence, then check for cancer mutations"

🤖 AI Assistant:I'll help you analyze TP53 step by step:

- 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
- gget_ref: Get reference genome information from Ensembl

- gget_blast: BLAST nucleotide or amino acid sequences
- gget_blat: Find genomic locations of sequences
- gget_muscle: Align multiple sequences

- gget_archs4: Get gene expression data from ARCHS4
- gget_enrichr: Perform gene set enrichment analysis

- gget_pdb: Fetch protein structure data from PDB
- gget_alphafold: Predict protein structure using AlphaFold

- gget_cosmic: Search COSMIC database for cancer mutations

- gget_cellxgene: Query single-cell RNA-seq data from CellxGene

# Download and install uv curl -LsSf https://astral.sh/uv/install.sh | sh # Verify installation uv --version uvx --version

uvx is a very nice tool that can run a python package installing it if needed.

You can run the gget-mcp server directly using uvx without cloning the repository:

# Run the server in HTTP mode (default) uvx gget-mcp http

STDIO Mode (for MCP clients that require stdio)

# Run the server in stdio mode uvx gget-mcp stdio

# Run the server in streamable HTTP mode on default (3002) port uvx gget-mcp http # Run on a specific port uvx gget-mcp http --port 8000

# Run the server in SSE mode uvx gget-mcp sse

In cases when there are problems with uvx often they can be caused by cleaning uv cache:

The HTTP mode will start a web server that you can access athttp://localhost:3002/mcp(with documentation athttp://localhost:3002/docs). The STDIO mode is designed for MCP clients that communicate via standard input/output, while SSE mode uses Server-Sent Events for real-time communication.

Note:Currently, we do not have a Swagger/OpenAPI interface, so accessing the server directly in your browser will not show much useful information. To explore the available tools and capabilities, you should either use the MCP Inspector (see below) or connect through an MCP client to see the available tools.

Configuring your AI Client (Anthropic Claude Desktop, Cursor, Windsurf, etc.)

We provide preconfigured JSON files for different use cases. Here are the actual configuration examples:

Use this configuration for most AI clients. Use this mode when you want to save large output files (sequences, structures, alignments) to disk instead of returning them as text. Create or update your MCP configuration file:

If you want to inspect the methods provided by the MCP server, use npx (you may need to install nodejs and npm):

npx @modelcontextprotocol/inspector --config mcp-config.json --server gget-mcp

You can also run the inspector manually and configure it through the interface:

After that you can explore the tools and resources with MCP Inspector at which is usually at 6274 port (note, if you run inspector several times it can change port)

Claude Desktop + gget_mcp Step-by-Step Guide (Windows)

This guide will walk you through setting up Claude Desktop with the gget_mcp extension and Google Drive integration on Windows. By the end, you'll be able to use Claude to fetch biological data (like gene sequences) and save them directly to your Google Drive folder with offline access.

- Windows PC with administrator access
- Google account
- Stable internet connection

Step 1: Set Up Google Drive for Desktop with Offline Access

Connect your project's shared Google account (if applicable)

Configure offline access for your working folder:

- Navigate to the folder you want to work with in Google Drive
- Right-click on the folder (e.g., "work" or your project folder)
- Select"Available offline"from the context menu
- This makes the folder accessible at a path likeC:\GDrive\holy-bio-mcp\My Disk\work

Important:This is different from just syncing - offline access ensures the files are locally available while still being part of your Google Drive structure.

powershell -c "irm https://astral.sh/uv/install.ps1 | iex"

Restart your terminal after installation

Both methods work equally well - choose whichever you prefer.

Step 5: Verify Installation & Cache Packages

Open Command Prompt or PowerShell and run:

- The command should start without errors
- Packages will be downloaded and cached
- If it runs successfully, everything is configured correctly
- You can pressCtrl+Cto stop it
- Open Claude Desktop
- Go toSettings(gear icon)
- Navigate to the"Extensions"tab in the left sidebar
- Enable theFilesystemExtension
- Add your Google Drive offline folder to the allowed directories (e.g.,C:\GDrive\holy-bio-mcp\My Disk\work)

Note:The Filesystem extension is built into Claude Desktop and uses MCP under the hood, but it's managed directly by the application. You don't need to configure it in the JSON file.
- In the same manner, go toSettings, navigate to the"Developer"tab in the left sidebar
- InDevelopersettings tab, click"Edit Config"button
- This will open theclaude_desktop_config.jsonfile
- Edit it and add the gget_mcp server configuration: