setup-tooluniverse

What the source does

• FilesystemNone observedNo reads or writes in the source
• NetworkDeclared1 observation
• ShellDeclared2 observations
• DependenciesPinnedNothing floats
• SecretsNone foundNo keys in source

Five audit layers

Gates applied: no behavioural pass.

__import__(package)

__import__(package)

# Add to PATH in ~/.zshrc or ~/.bashrc

# or add to PATH: export PATH="$HOME/.local/bin:$PATH"

curl -LsSf https://astral.sh/uv/install.sh | sh

curl -LsSf https://astral.sh/uv/install.sh | sh

- If uvx is missing, install uv: `curl -LsSf https://astral.sh/uv/install.sh | sh`

curl -LsSf https://astral.sh/uv/install.sh | sh

curl -LsSf https://astral.sh/uv/install.sh | sh

Audit 0.4.1 · source sha 43be0fac747b · 28 Oct 2026Report an issue or request a re-scan

• Publishermims-harvard GitHub organizationOwner of the repository this skill is read from
• Source foldermims-harvard/tooluniverse/skills/setup-tooluniverseThe exact folder we audited
• LicenceApache-2.0As the repository states it
• Commit pinned for this verdict43be0fac747bA new audit runs when the source changes
• Repository statusNot archivedPushed today
• Sandboxed runNot runSkills are read, not executed; layer L4 is skipped

Its description: Install and configure ToolUniverse for any use case — MCP server (chat-based), CLI (command line with 14 subcommands), or Python SDK (Coding API with 3 calling patterns). Covers uv/uvx setup, MCP configuration for 12+…

---
name: setup-tooluniverse
description: Install and configure ToolUniverse for any use case — MCP server (chat-based), CLI (command line with 14 subcommands), or Python SDK (Coding API with 3 calling patterns). Covers uv/uvx setup, MCP configuration for 12+ AI clients (Cursor, Claude Desktop, Windsurf, VS Code, Codex, Gemini CLI, Trae, Cline, etc.), full CLI reference (tu list/grep/info/find/run/test/status/build/remote/doctor/serve/connect/connections/disconnect), Coding API quickstart, agentic tools, code executor, API key walkthrough, skill installation, and upgrading. Use when user asks how to set up ToolUniverse, which access mode to use (MCP vs CLI vs SDK), configuring MCP servers, using the CLI, troubleshooting installation, upgrading, or mentions installing ToolUniverse or setting up scientific tools. Also triggers for "how do I use ToolUniverse", "what's the best way to access tools", "command line", "tu command", "coding API", "tu build".
---

# Setup ToolUniverse

Guide the user step-by-step through setting up ToolUniverse.

## Agent Behavior

- **Detect language** from user's first message. Respond in their language; keep commands/URLs in English.
- Go **one step at a time**. Ask before proceeding.
- Use **AskQuestion** for structured choices.
- **Explain briefly** in plain language. Celebrate small wins.
- When something goes wrong, help troubleshoot before moving on.

## Internal Notes (do not show)

ToolUniverse has 2,700+ tools. The `tooluniverse` command enables compact mode automatically, exposing only 5 core MCP tools (list_tools, grep_tools, get_tool_info, execute_tool, find_tools) while keeping all tools accessible via execute_tool.

## What is ToolUniverse?

**Always explain first, in plain language:**

ToolUniverse is free, open-source software connecting to 2,000+ scientific databases (PubMed, UniProt, ChEMBL, FAERS, ClinicalTrials.gov, etc.). Instead of visiting each website, you search from one place. Think of it like a universal remote for scientific databases.

**Why AI assistants?** The AI reads your question, figures out which databases to search, runs queries, and summarizes results. You just ask your question.

## Step 1: Choose How to Use It

Present using AskQuestion:

| Mode | What it means | Who it's for |
|------|---------------|-------------|
| **Chat mode** | Ask questions to an AI assistant. No coding. | Most researchers. |
| **Command line** | Type short commands in Terminal. | Quick tests. Terminal-comfortable users. |
| **Python code** | Write scripts for automated pipelines. | Programmers. |

Options: "I want to ask questions" → Chat mode | "Quick try" → CLI | "I write Python" → SDK | "I don't know" → Recommend Chat mode

**If Chat mode**, ask which app (AskQuestion): Cursor, Claude Desktop, VS Code/Copilot, Windsurf, Claude Code, Gemini CLI, Codex, Cline/Trae/Antigravity/OpenCode. "I don't have any" → Recommend [Claude Desktop](https://claude.ai/download).

## Step 2: Install uv

Only prerequisite: `uv` (manages everything else automatically).

**Terminal help** (if needed): Mac: Cmd+Space → "Terminal" → Enter. Windows: Win key → "PowerShell" → Enter.

```bash
curl -LsSf https://astral.sh/uv/install.sh | sh
```
(This is a safe, standard command that downloads and installs `uv`, a small package manager. It's widely used by Python developers. Close and reopen your terminal after it finishes.)

Verify: `uv --version`

## CLI Setup

Make sure Step 2 is done, then try:

```bash
uvx --from tooluniverse tu status              # How many tools?
uvx --from tooluniverse tu find 'drug safety'  # Search by topic
uvx --from tooluniverse tu info FAERS_count_death_related_by_drug  # See params
uvx --from tooluniverse tu run FAERS_count_death_related_by_drug '{"medicinalproduct": "metformin"}'
```

First run takes ~30s (downloads package), then instant. **Shortcut**: `uv tool install tooluniverse` → then just use `tu` directly.

### All CLI subcommands

| Command | What it does | Example |
|---------|-------------|---------|
| `tu status` | Show tool count and top categories | `tu status` |
| `tu list` | List tools (modes: names, categories, basic, by_category, summary, custom) | `tu list --mode basic --limit 20` |
| `tu find` | Search by natural language (keyword scoring, no API key needed) | `tu find 'protein structure analysis'` |
| `tu grep` | Text/regex pattern search | `tu grep '^UniProt' --mode regex` |
| `tu info` | Show tool parameters and schema | `tu info PubMed_search_articles` |
| `tu run` | Execute a tool | `tu run PubMed_search_articles '{"query": "CRISPR"}'` |
| `tu test` | Test a tool with its example inputs | `tu test UniProt_get_entry_by_accession` |
| `tu build` | Generate typed Python wrappers for Coding API (also regenerates the internal lazy-load registry in place — unaffected by `--output`) | `tu build --output ./my_tools` |
| `tu serve` | Start MCP stdio server (same as `uvx tooluniverse`) | `tu serve` |

**Output flags** (most commands except `build`/`serve`): `--json` (pretty) or `--raw` (compact, pipe-friendly).

Continue to **Step 3** (API Keys).

## SDK Setup

> **Install `uv` first (Step 2). Do not use system `pip`.** On a current Mac
> (Homebrew Python 3.13/3.14) `pip install tooluniverse` stops with
> `error: externally-managed-environment` (PEP 668), and `python3 -m venv` can
> fail at `ensurepip`. `uv` avoids both because it downloads and manages its own
> Python.

```bash
uv venv --python 3.12          # own Python + virtualenv, ignores system pip
source .venv/bin/activate      # Windows: .venv\Scripts\activate
uv pip install tooluniverse
```

`uv pip install` needs an active virtualenv — run `uv venv` first, or use
`uv tool install tooluniverse` if you only want the `tu` command.

For detailed patterns, invoke the `tooluniverse-sdk` skill.

**Optional extras**: the base install covers API/database tools. Local ML,
cheminformatics, and plotting tools need extras — `uv pip install
'tooluniverse[ml]'`, `[visualization]`, `[

Excerpt, first 6,000 characters of SKILL.md, verbatim from the audited commit. It is text from someone else’s repository, quoted so you can judge it before your agent reads it.

1. 2026-10-28
   !CAUTION B 89 / 100

   first audit · source 43be0fac747b

Questions about setup-tooluniverse

• github.com/mims-harvard/tooluniverse/tree/main/skills/setup-tool — the audited source at commit 43be0fac747b and every finding aboveObserved · 28 Oct 2026

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