#!/usr/bin/env node
// src/index.ts
import { Server } from '@modelcontextprotocol/sdk/server/index.js';
import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
import {
ListToolsRequestSchema,
CallToolRequestSchema,
ErrorCode,
McpError,
} from '@modelcontextprotocol/sdk/types.js';
import { AlphaGenomeClient } from './alphagenome-client.js';
import { ApiKeyError, RateLimitError, ValidationError } from './types.js';
import { ALL_TOOLS } from './tools.js';
import {
validateInput,
variantPredictionSchema,
regionAnalysisSchema,
batchScoreSchema,
} from './utils/validation.js';
import { formatVariantResult, formatRegionResult, formatBatchResult } from './utils/formatting.js';
import type { VariantPredictionParams, RegionAnalysisParams, BatchScoreParams } from './types.js';
/**
* AlphaGenome MCP Server
*
* Integrates Google DeepMind's AlphaGenome with Claude Desktop
* for AI-powered genomic variant analysis.
*
* Uses AlphaGenome Python SDK via subprocess bridge for real-time predictions.
*/
// Parse command-line arguments for API key
function parseApiKey(): string | undefined {
const args = process.argv.slice(2);
const apiKeyIndex = args.indexOf('--api-key');
if (apiKeyIndex !== -1 && apiKeyIndex + 1 < args.length) {
return args[apiKeyIndex + 1];
}
return undefined;
}
const CLI_API_KEY = parseApiKey();
// Create MCP server
const server = new Server(
{
name: 'alphagenome-mcp',
version: '0.1.5',
},
{
capabilities: {
tools: {},
},
}
);
// Initialize AlphaGenome client (lazy initialization)
let client: AlphaGenomeClient | null = null;
/**
* Get or create AlphaGenome client instance
*/
function getClient(): AlphaGenomeClient {
if (!client) {
try {
// Use CLI API key if provided, otherwise fall back to env var
client = new AlphaGenomeClient(CLI_API_KEY);
} catch (error) {
if (error instanceof ApiKeyError) {
console.error('\n❌ AlphaGenome API Key Error:\n');
console.error(error.message);
console.error('\nTo fix this:');
console.error('1. Get an API key from https://alphagenome.deepmind.com');
console.error('2. Provide it via command-line:');
console.error(' --api-key YOUR_API_KEY');
console.error('3. Or set it in your environment or Claude config:');
console.error(' export ALPHAGENOME_API_KEY=your-key-here');
console.error('4. Or use mock mode for testing: ALPHAGENOME_API_KEY=mock\n');
process.exit(1);
}
throw error;
}
}
return client;
}
// ============================================================================
// MCP Request Handlers
// ============================================================================
/**
* Handle ListTools request - return available tools
*/
server.setRequestHandler(ListToolsRequestSchema, async () => {
return { tools: ALL_TOOLS };
});
/**
* Handle CallTool request - execute tool and return results
*/
server.setRequestHandler(CallToolRequestSchema, async (request) => {
const { name, arguments: args } = request.params;
try {
switch (name) {
case 'predict_variant_effect': {
// Validate input
const params = validateInput(variantPredictionSchema, args) as VariantPredictionParams;
// Call AlphaGenome API
const result = await getClient().predictVariant(params);
// Format output
const formatted = formatVariantResult(result);
return {
content: [
{
type: 'text',
text: formatted,
},
],
};
}
case 'batch_score_variants': {
const params = validateInput(batchScoreSchema, args) as BatchScoreParams;
const result = await getClient().batchScore(params);
const formatted = formatBatchResult(result);
return {
content: [
{
type: 'text',
text: formatted,
},
],
};
}
case 'assess_pathogenicity': {
const params = validateInput(variantPredictionSchema, args) as VariantPredictionParams;
const result = await getClient().assessPathogenicity(params);
return {
content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],
};
}
case 'predict_tissue_specific': {
const result = await getClient().predictTissueSpecific(args);
return {
content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],
};
}
case 'compare_variants': {
const result = await getClient().compareVariants(args);
return {
content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],
};
}
case 'predict_splice_impact': {
const params = validateInput(variantPredictionSchema, args) as VariantPredictionParams;
const result = await getClient().predictSpliceImpact(params);
return {
content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],
};
}
case 'predict_expression_impact': {
const params = validateInput(variantPredictionSchema, args) as VariantPredictionParams;
const result = await getClient().predictExpressionImpact(params);
return {
content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],
};
}
case 'analyze_gwas_locus': {
const result = await getClient().analyzeGwasLocus(args);
return {
content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],
};
}
case 'compare_alleles': {
const result = await getClient().compareAlleles(args);
return {
content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],
};
}
case 'batch_tissue_comparison': {
const result = await getClient().batchTissueComparison(args);
return {
content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],
};
}
case 'predict_tf_binding_impact': {
const params = validateInput(variantPredictionSchema, args) as VariantPredictionParams;
const result = await getClient().predictTfBindingImpact(params);
return {
content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],
};
}
case 'predict_chromatin_impact': {
const params = validateInput(variantPredictionSchema, args) as VariantPredictionParams;
const result = await getClient().predictChromatinImpact(params);
return {
content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],
};
}
case 'compare_protective_risk': {
const result = await getClient().compareProtectiveRisk(args);
return {
content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],
};
}
case 'batch_pathogenicity_filter': {
const result = await getClient().batchPathogenicityFilter(args);
return {
content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],
};
}
case 'compare_variants_same_gene': {
const result = await getClient().compareVariantsSameGene(args);
return {
content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],
};
}
case 'predict_allele_specific_effects': {
const params = validateInput(variantPredictionSchema, args) as VariantPredictionParams;
const result = await getClient().predictAlleleSpecificEffects(params);
return {
content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],
};
}
case 'annotate_regulatory_context': {
const params = validateInput(variantPredictionSchema, args) as VariantPredictionParams;
const result = await getClient().annotateRegulatoryContext(params);
return {
content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],
};
}
case 'batch_modality_screen': {
const result = await getClient().batchModalityScreen(args);
return {
content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],
};
}
case 'generate_variant_report': {
const params = validateInput(variantPredictionSchema, args) as VariantPredictionParams;
const result = await getClient().generateVariantReport(params);
return {
content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],
};
}
case 'explain_variant_impact': {
const params = validateInput(variantPredictionSchema, args) as VariantPredictionParams;
const result = await getClient().explainVariantImpact(params);
return {
content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],
};
}
default:
throw new McpError(ErrorCode.MethodNotFound, `Unknown tool: ${name}`);
}
} catch (error: unknown) {
// Handle different error types with appropriate MCP error codes
if (error instanceof McpError) {
throw error;
}
if (error instanceof Error) {
// Validation errors
if (error.message.includes('Validation error')) {
throw new McpError(ErrorCode.InvalidParams, `Input validation failed:\n${error.message}`);
}
// API errors
if (error instanceof ApiKeyError) {
throw new McpError(ErrorCode.InternalError, `API key error: ${error.message}`);
}
if (error instanceof RateLimitError) {
throw new McpError(ErrorCode.InternalError, `Rate limit exceeded: ${error.message}`);
}
if (error instanceof ValidationError) {
throw new McpError(ErrorCode.InvalidParams, `Validation error: ${error.message}`);
}
// Generic error
throw new McpError(ErrorCode.InternalError, `An unexpected error occurred: ${error.message}`);
}
// Unknown error type
console.error('Unexpected error:', error);
throw new McpError(
ErrorCode.InternalError,
'An unexpected error occurred. Please check server logs.'
);
}
});
// ============================================================================
// Server Startup
// ============================================================================
/**
* Main server startup function
*/
async function main() {
const transport = new StdioServerTransport();
await server.connect(transport);
console.error('AlphaGenome MCP Server running on stdio');
}
// Start the server
main().catch((error) => {
console.error('❌ Fatal error starting server:', error);
process.exit(1);
});
