@biomate/mcp-server 0.1.0

package/README.md

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+# @biomate/mcp-server
+
+BioMate MCP server — exposes 19 scientific workflow tools to any MCP-compatible AI host (Claude Code, Claude Desktop, Cursor, Codex CLI).
+
+## Install
+
+Add to your Claude Code or Claude Desktop config:
+
+**`~/.mcp.json`** (Claude Code):
+```json
+{
+  "mcpServers": {
+    "biomate": {
+      "command": "npx",
+      "args": ["-y", "@biomate/mcp-server"],
+      "env": {
+        "BIOMATE_API_KEY": "bm_live_your_key_here"
+      }
+    }
+  }
+}
+```
+
+Get your API key at **[dev-public.biomate.ai/account/api-keys](https://dev-public.biomate.ai/account/api-keys)**.
+
+## Tools (19)
+
+| Tool | Purpose |
+|---|---|
+| `biomate_session` | Primary: natural-language goal → full workflow execution |
+| `search_workflow` | Search 2,455 indexed workflows by natural language |
+| `get_workflow_spec` | Full parameter spec for a workflow |
+| `run_workflow` | Execute with explicit parameters |
+| `get_run` / `watch_run` | Status, phases, steps, outputs |
+| `cancel_run` | Cancel a running job |
+| `list_runs` | History with filters |
+| `preview_file` | Server-side preview of output files |
+| `export_report` | PDF/markdown publication report |
+| `analyze_results` | AI interpretation of findings |
+| `explain_error` | Root-cause diagnosis for failed runs |
+| `query_database` | UniProt, PDB, NCBI, ChEMBL, AlphaFold |
+| `resolve_accession` | GEO/SRA/ENA → auto-run GEO data connector |
+| `browse_data` / `fetch_public_data` | Browse and stage public datasets |
+| `upload_file` | Get signed S3 PUT URL for local uploads |
+| `recall_memory` | Retrieve relevant prior runs and procedures |
+| `search_literature` | PubMed, Semantic Scholar, OpenAlex |
+
+## Environment variables
+
+| Variable | Description |
+|---|---|
+| `BIOMATE_API_KEY` | Personal API key (`bm_live_xxx`) — required |
+| `BIOMATE_API_BASE` | BioMate server URL (default: `https://dev-public.biomate.ai`) |
+
+## Example
+
+```
+> Screen aspirin and caffeine for hERG inhibition and CYP3A4 metabolism.
+```
+
+```
+> Run RNA-seq differential expression on s3://bucket/exp1/ — human GRCh38, treated vs control.
+```
+
+```
+> Fetch GSE183947 from GEO and run the DESeq2 pipeline.
+```
+
+## License
+
+MIT — this package only. BioMate platform usage governed by [biomate.ai/terms](https://biomate.ai/terms).

package/dist/index.d.ts

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+#!/usr/bin/env node
+/**
+ * @biomate/mcp-server
+ *
+ * MCP stdio server that exposes BioMate's scientific workflow capabilities
+ * to any MCP-compatible AI host (Claude Code, Claude Desktop, Cursor, Codex CLI).
+ *
+ * Configuration (environment variables):
+ *   BIOMATE_API_BASE   BioMate server URL (default: https://dev-public.biomate.ai)
+ *   BIOMATE_API_KEY    Personal API key (bm_live_xxx) from biomate.ai/account/api-keys
+ *   BIOMATE_REFRESH_TOKEN  OAuth refresh token (alternative to API key)
+ *
+ * Each tool call POSTs to ${BIOMATE_API_BASE}/tools/${toolName} with the
+ * Authorization header set. The /tools/* routes are served by BioMate's
+ * Node.js API server.
+ */
+export {};

package/dist/index.js

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+#!/usr/bin/env node
+/**
+ * @biomate/mcp-server
+ *
+ * MCP stdio server that exposes BioMate's scientific workflow capabilities
+ * to any MCP-compatible AI host (Claude Code, Claude Desktop, Cursor, Codex CLI).
+ *
+ * Configuration (environment variables):
+ *   BIOMATE_API_BASE   BioMate server URL (default: https://dev-public.biomate.ai)
+ *   BIOMATE_API_KEY    Personal API key (bm_live_xxx) from biomate.ai/account/api-keys
+ *   BIOMATE_REFRESH_TOKEN  OAuth refresh token (alternative to API key)
+ *
+ * Each tool call POSTs to ${BIOMATE_API_BASE}/tools/${toolName} with the
+ * Authorization header set. The /tools/* routes are served by BioMate's
+ * Node.js API server.
+ */
+import { Server } from "@modelcontextprotocol/sdk/server/index.js";
+import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
+import { CallToolRequestSchema, ListToolsRequestSchema, } from "@modelcontextprotocol/sdk/types.js";
+import { createRequire } from "module";
+const require = createRequire(import.meta.url);
+// ── Config ────────────────────────────────────────────────────────────────────
+const API_BASE = (process.env.BIOMATE_API_BASE ?? "https://dev-public.biomate.ai").replace(/\/$/, "");
+const API_KEY = process.env.BIOMATE_API_KEY ?? process.env.BIOMATE_REFRESH_TOKEN ?? "";
+// ── Tools manifest ────────────────────────────────────────────────────────────
+const manifest = require("./tools_manifest.json");
+const TOOLS = manifest.mcp.map((t) => ({
+    name: t.name,
+    description: t.description,
+    inputSchema: t.inputSchema,
+}));
+// ── Server ────────────────────────────────────────────────────────────────────
+const server = new Server({ name: "biomate", version: "2.0.0" }, { capabilities: { tools: {} } });
+server.setRequestHandler(ListToolsRequestSchema, async () => ({ tools: TOOLS }));
+server.setRequestHandler(CallToolRequestSchema, async (req) => {
+    const { name, arguments: args } = req.params;
+    const headers = {
+        "Content-Type": "application/json",
+    };
+    if (API_KEY) {
+        headers["Authorization"] = `Bearer ${API_KEY}`;
+    }
+    let data;
+    let ok = true;
+    try {
+        const res = await fetch(`${API_BASE}/tools/${name}`, {
+            method: "POST",
+            headers,
+            body: JSON.stringify(args ?? {}),
+            signal: AbortSignal.timeout(120_000),
+        });
+        ok = res.ok;
+        try {
+            data = await res.json();
+        }
+        catch {
+            data = { error: `HTTP ${res.status}: ${res.statusText}` };
+            ok = false;
+        }
+    }
+    catch (err) {
+        const msg = err instanceof Error ? err.message : String(err);
+        data = { error: msg };
+        ok = false;
+    }
+    return {
+        content: [{ type: "text", text: JSON.stringify(data, null, 2) }],
+        isError: !ok,
+    };
+});
+// ── Start ─────────────────────────────────────────────────────────────────────
+if (!API_KEY) {
+    process.stderr.write("[biomate-mcp] WARNING: BIOMATE_API_KEY not set. " +
+        "Get your key at https://dev-public.biomate.ai/account/api-keys\n");
+}
+const transport = new StdioServerTransport();
+await server.connect(transport);