👤 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:

[Uses gget_search] → Found TP53 (ENSG00000141510) on chromosome 17
[Uses gget_info] → TP53 is a protein-coding tumor suppressor gene
[Uses gget_seq with translate=True] → Retrieved 393 amino acid protein sequence
[Uses gget_cosmic] → Found hotspot mutations R175H, R248Q, R273H in multiple cancers

👤 User: "Now predict the 3D structure of this protein sequence: MSKGEELFTGVVPILVEL..."

🤖 AI Assistant: Let me analyze this sequence:

[Uses gget_blast] → Identified as Green Fluorescent Protein (GFP)
[Uses gget_alphafold] → Predicted classic beta-barrel structure with 90%+ confidence

👤 User: "Perform pathway enrichment for DNA repair genes: TP53, BRCA1, BRCA2, ATM"

🤖 AI Assistant: [Uses gget_enrichr] → Top pathways: DNA Damage Response, Homologous Recombination, Cell Cycle Checkpoints, p53 Signaling

See how powerful this is? You can now ask natural language questions about genes, sequences, mutations, and pathways - the AI does the complex bioinformatics work for you!

MCP is a protocol that bridges the gap between AI systems and specialized domain tools. It enables:

• Structured Access: Direct connection to powerful bioinformatics tools and databases
• Natural Language Queries: Simplified interaction with complex genomics workflows
• Type Safety: Strong typing and validation through FastMCP
• AI Integration: Seamless integration with AI assistants and agents

If you want to understand more about what the Model Context Protocol is and how to use it more efficiently, you can take the DeepLearning AI Course or search for MCP videos on YouTube.

Gene Information & Search

• 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

Sequence Analysis

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

Expression & Functional Analysis

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

Protein Structure & Function

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

Cancer & Mutation Analysis

• gget_cosmic: Search COSMIC database for cancer mutations

Single-cell Analysis

• 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.

STDIO Mode (for MCP clients that require stdio)

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

HTTP Mode (Web Server)

# 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

SSE Mode (Server-Sent Events)

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

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

For STDIO mode with uvx:

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

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

npx @modelcontextprotocol/inspector

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)

Overview

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.

Prerequisites

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

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

1. Download and install Google Drive for Desktop

2. Launch the application and sign in with your user account

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

4. 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 like C:\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.

Step 2: Install Claude Desktop

1. Download Claude Desktop for Windows
2. Run the installer and follow the setup wizard
3. Sign in with your Anthropic/Claude account
4. Complete the initial setup

Step 3: Install uv Package Manager

1. Install uv using one of these methods:

   Option A: Using winstall

   • Visit https://winstall.app/apps/astral-sh.uv
   • Follow installation instructions

   Option B: Using PowerShell

   powershell

   Copy

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

2. Restart your terminal after installation

Step 4: Install Node.js

You can install Node.js using either method:

Option A: Native Installer

1. Visit https://nodejs.org/en/download
2. Download the Windows installer (LTS version recommended)
3. Run the installer with default settings

Option B: Using Chocolatey

choco install nodejs

Both methods work equally well - choose whichever you prefer.

Step 5: Verify Installation & Cache Packages

Open Command Prompt or PowerShell and run:

uvx --from gget-mcp@latest stdio

Expected behavior:

• The command should start without errors
• Packages will be downloaded and cached
• If it runs successfully, everything is configured correctly
• You can press Ctrl+C to stop it

Step 6: Configure Claude Desktop

6.1: Enable Filesystem Extension

1. Open Claude Desktop
2. Go to Settings (gear icon)
3. Navigate to the "Extensions" tab in the left sidebar
4. Enable the Filesystem Extension
5. 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.

6.2: Add gget_mcp Server

1. In the same manner, go to Settings, navigate to the "Developer" tab in the left sidebar
2. In Developer settings tab, click "Edit Config" button
3. This will open the claude_desktop_config.json file
4. Edit it and add the gget_mcp server configuration:

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

5. Save the configuration file

Step 7: Restart Claude Desktop

1. Completely close Claude Desktop (check system tray)
2. Restart the application
3. Note: On first launch, you might experience a timeout - this is normal
4. If needed, restart Claude Desktop a second time

Step 8: Verify Extensions Are Active

1. Open Claude Desktop Settings
2. Go to the Developer tab
3. Confirm that both components are enabled:
   • ✅ Filesystem Extension - should show your configured Google Drive path and show "Running" status
   • ✅ gget MCP Server - should show "Running" status

Step 9: Test the Setup

Now let's verify everything works! In Claude Desktop, create a new chat. Click "Search and tools" icon, select and enable both gget_mcp and filesystem

Try this prompt:

Please search for the COL1A1 gene, retrieve its protein sequence, 
and save it to C:\GDrive\holy-bio-mcp\My Disk\work\test_sequences\ as a FASTA file.

Expected result:

• Claude will use gget_mcp to search for the gene
• It will fetch the sequence data
• It will save the file to your specified folder
• The file will sync to Google Drive automatically
• Claude will be able to read it using Filesystem Extension.

Troubleshooting

MCP Server Not Connecting

• Ensure uv and node are in your system PATH
• Try running the verification command again from Step 5
• Restart Claude Desktop completely

Filesystem Permission Errors

• Check that the Filesystem Extension has access to your Google Drive folder
• Verify the folder has offline access enabled in Google Drive
• Try running Claude Desktop as administrator
• Ensure the path is correct (use the exact path shown in File Explorer)

Timeout on First Launch

• This is normal - simply restart Claude Desktop
• Wait 10-15 seconds before making requests

gget Commands Not Working

• Ensure internet connection is stable (gget fetches from online databases)
• Check that the gget_mcp server shows as "Active" in settings
• Try the verification command from Step 5 again

Google Drive Offline Access Issues

• Confirm the folder shows a green checkmark in Google Drive for Desktop
• If files aren't syncing, right-click the folder and re-enable "Available offline"
• Check that you have enough local disk space for offline files

Success! 🎉

If everything works correctly, you now have:

• ✅ Claude Desktop with MCP capabilities
• ✅ Access to biological databases via gget_mcp
• ✅ Direct file operations in your Google Drive offline folder
• ✅ Automatic cloud synchronization of all results

You can now ask Claude to fetch gene sequences, protein data, perform BLAST searches, and save everything directly to your Google Drive folder with offline access!

Example Use Cases

• Fetch gene sequences: "Get the DNA sequence for BRCA1 and save it to my Drive"
• Protein analysis: "Find the protein sequence for TP53 and create a markdown report"
• Bulk operations: "Search for all genes related to apoptosis and create a summary table"
• Cross-referencing: "Get information about COL1A1 from Ensembl and UniProt"

Additional Resources

• gget documentation
• Model Context Protocol docs
• Claude Desktop support

Guide updated: October 13, 2025

# Clone the repository
git clone https://github.com/longevity-genie/gget-mcp.git
cd gget-mcp
uv sync

Running the MCP Server

If you already cloned the repo you can run the server with uv:

# Start the MCP server locally (HTTP mode)
uv run server

# Or start in STDIO mode  
uv run stdio

# Or start in SSE mode
uv run sse

The MCP server is provided with comprehensive tests including both unit tests and integration tests for network-dependent operations.

Running Tests

Run tests for the MCP server:

# Run all tests (excluding expensive judge tests)
uv run pytest -vvv -m "not judge"

# Run only fast tests (skip slow, integration, and judge tests)
uv run pytest -vvv -m "not slow and not integration and not judge"

# Run only integration tests
uv run pytest -vvv -m integration

# Run judge tests (expensive LLM tests - requires API keys and may cost money)
uv run pytest test/test_judge.py -vvv

# Run tests with coverage (excluding judge tests)
uv run pytest -vvv --cov=src/gget_mcp --cov-report=term-missing -m "not judge"

Note on Judge Tests: The judge tests (test_judge.py) use large language models to evaluate the AI agent's performance with gget tools. These tests:

• Are automatically excluded from CI/CD to avoid costs
• Require API keys (GEMINI_API_KEY or similar)
• May incur charges from LLM API providers
• Are designed for local development and manual evaluation
• Provide valuable insights into how well the tools work with AI agents

GitHub Actions Workflows

This project includes several GitHub Actions workflows:

• CI (.github/workflows/ci.yml): Runs on every push/PR with basic linting and fast tests
• Tests (.github/workflows/test.yml): Comprehensive testing across multiple OS and Python versions
  • Fast tests on all platforms
  • Integration tests (may require network access)
  • Slow tests (like BLAST operations) - runs only on Ubuntu with Python 3.11
  • Code coverage reporting
  • Security checks with bandit and safety
• Publish (.github/workflows/publish.yml): Publishes to PyPI when tags are pushed

You can use MCP inspector with locally built MCP server same way as with uvx.

External Dependencies

Some gget functions depend on external web services and databases that may occasionally be unavailable or rate-limited. The server implements proper error handling and retries where appropriate.

Test Coverage

While we provide comprehensive tests including integration tests for network-dependent operations, some test cases may be sensitive to external service availability. Some automated test results may need manual validation.