# Claude Desktop Installation Guide
This document explains how to configure the AGR MCP Server with Claude Desktop.
## Prerequisites
- Node.js 18 or higher
- Claude Desktop application installed
- This AGR MCP Server project cloned locally
## Installation Options
### Option 1: Global NPM Installation (Recommended)
```bash
# Install globally via npm
npm install -g agr-mcp-server-enhanced
# Or run directly with npx (no installation)
npx agr-mcp-server-enhanced
```
### Option 2: Local Development Installation
```bash
cd /path/to/agr-mcp-server-js
npm install
npm run setup
```
## Configure Claude Desktop
### For Global Installation (Option 1)
**Configuration File Locations:**
- **macOS**: `~/Library/Application Support/Claude/claude_desktop_config.json`
- **Windows**: `%APPDATA%/Claude/claude_desktop_config.json`
- **Linux**: `~/.config/Claude/claude_desktop_config.json`
**Configuration Content:**
```json
{
"mcpServers": {
"agr-genomics-enhanced-js": {
"command": "agr-mcp-server",
"args": [],
"env": {
"LOG_LEVEL": "info"
}
}
}
}
```
### For Local Installation (Option 2)
```json
{
"mcpServers": {
"agr-genomics-enhanced-js": {
"command": "node",
"args": ["/path/to/agr-mcp-server-js/src/agr-server-enhanced.js"],
"cwd": "/path/to/agr-mcp-server-js",
"env": {
"LOG_LEVEL": "info"
}
}
}
}
```
**Important:** Replace `/path/to/agr-mcp-server-js` with the absolute path to your cloned repository.
### 4. Restart Claude Desktop
Close and reopen Claude Desktop for the configuration to take effect.
## Verification
Once configured, you should have access to these genomics tools in Claude Desktop:
- `search_genes` - Gene search with species filtering
- `get_gene_info` - Detailed gene information
- `get_gene_diseases` - Disease associations
- `search_diseases` - Disease search functionality
- `get_gene_expression` - Expression data across tissues
- `find_orthologs` - Cross-species orthology analysis
- `blast_sequence` - BLAST search with auto-detection
- `get_species_list` - Supported model organisms
- `get_cache_stats` - Performance monitoring
- `clear_cache` - Cache management
## Testing
You can test the server independently using these CLI commands:
```bash
# Test basic functionality
npm run query genes BRCA1
# Test disease search
npm run query diseases "breast cancer"
# Get gene information
npm run query info HGNC:1100
# Check server health
npm run health-check
```
## Troubleshooting
1. **Server not appearing in Claude Desktop:**
- Verify the absolute path in the configuration
- Check that Node.js is in your system PATH
- Restart Claude Desktop completely
2. **Permission errors:**
- Ensure the server files are readable
- Check Node.js execution permissions
3. **Connection issues:**
- Test the server with `npm start`
- Check logs with `LOG_LEVEL=debug npm start`
## Optional Configuration
You can customize the server behavior with these environment variables in the config:
```json
{
"mcpServers": {
"agr-genomics-enhanced-js": {
"command": "node",
"args": ["/path/to/agr-mcp-server-js/src/agr-server-enhanced.js"],
"cwd": "/path/to/agr-mcp-server-js",
"env": {
"LOG_LEVEL": "info",
"API_TIMEOUT": "30000",
"CACHE_TTL": "300",
"CACHE_MAX_KEYS": "1000"
}
}
}
}
```
