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2
Commits
| Author | SHA1 | Date | |
|---|---|---|---|
 promptadmin
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0f20c2709a | ||
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promptadmin
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1f0c27ea70 |
@@ -1,8 +1,8 @@
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---
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lineage_type: import
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upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/setup-tooluniverse/SKILL.md
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upstream_sha: e2520a96
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imported_at: 2026-06-26
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upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/089eb8e6/skills/setup-tooluniverse/SKILL.md
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upstream_sha: 089eb8e6
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imported_at: 2026-07-25
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prompt_class: catalogue
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upstream_changes: accepted
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name: setup-tooluniverse
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@@ -68,7 +68,7 @@ Make sure Step 2 is done, then try:
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uvx --from tooluniverse tu status # How many tools?
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uvx --from tooluniverse tu find 'drug safety' # Search by topic
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uvx --from tooluniverse tu info FAERS_count_death_related_by_drug # See params
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uvx --from tooluniverse tu run FAERS_count_death_related_by_drug '{"drug_name": "metformin"}'
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uvx --from tooluniverse tu run FAERS_count_death_related_by_drug '{"medicinalproduct": "metformin"}'
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```
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First run takes ~30s (downloads package), then instant. **Shortcut**: `uv tool install tooluniverse` → then just use `tu` directly.
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@@ -84,7 +84,7 @@ First run takes ~30s (downloads package), then instant. **Shortcut**: `uv tool i
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| `tu info` | Show tool parameters and schema | `tu info PubMed_search_articles` |
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| `tu run` | Execute a tool | `tu run PubMed_search_articles '{"query": "CRISPR"}'` |
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| `tu test` | Test a tool with its example inputs | `tu test UniProt_get_entry_by_accession` |
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| `tu build` | Generate typed Python wrappers for Coding API | `tu build --output ./my_tools` |
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| `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` |
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| `tu serve` | Start MCP stdio server (same as `uvx tooluniverse`) | `tu serve` |
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**Output flags** (most commands except `build`/`serve`): `--json` (pretty) or `--raw` (compact, pipe-friendly).
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@@ -93,12 +93,30 @@ Continue to **Step 3** (API Keys).
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## SDK Setup
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Make sure Step 2 is done. For detailed patterns, invoke the `tooluniverse-sdk` skill.
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> **Install `uv` first (Step 2). Do not use system `pip`.** On a current Mac
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> (Homebrew Python 3.13/3.14) `pip install tooluniverse` stops with
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> `error: externally-managed-environment` (PEP 668), and `python3 -m venv` can
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> fail at `ensurepip`. `uv` avoids both because it downloads and manages its own
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> Python.
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```bash
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uv venv --python 3.12 # own Python + virtualenv, ignores system pip
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source .venv/bin/activate # Windows: .venv\Scripts\activate
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uv pip install tooluniverse
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```
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`uv pip install` needs an active virtualenv — run `uv venv` first, or use
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`uv tool install tooluniverse` if you only want the `tu` command.
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For detailed patterns, invoke the `tooluniverse-sdk` skill.
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**Optional extras**: the base install covers API/database tools. Local ML,
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cheminformatics, and plotting tools need extras — `uv pip install
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'tooluniverse[ml]'`, `[visualization]`, `[bioinformatics]`, or `[all]`.
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Run `tooluniverse-doctor` to see which groups you are missing.
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Note `[all]` does **not** include `singlecell`, `smolagents`, `client`, or
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`build`; install those separately.
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### Coding API — 3 calling patterns
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**Pattern 1: Direct import** (typed, with autocomplete):
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@@ -130,9 +148,33 @@ Continue to **Step 3** (API Keys).
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## MCP Setup (Chat Mode)
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Make sure Step 2 is done (`uv --version` works).
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**Offer the two low-effort paths first.** Editing JSON by hand is the fallback,
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not the recommendation — a mistyped comma is the single most common setup
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failure. Only walk through the manual path if neither option below fits.
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### Add ToolUniverse to your app's config
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**Path A — let an AI agent do it.** If the user already has any agent (Claude,
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Cursor, Copilot, Gemini, Codex...), they can paste this into it:
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```
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Read https://aiscientist.tools/setup.md and set up ToolUniverse for me.
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```
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The agent handles config, keys, skills, and validation. No terminal, no JSON.
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**Path B — Claude Code users: one-liner, no config file at all.**
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```bash
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claude plugin marketplace add mims-harvard/ToolUniverse
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claude plugin install tooluniverse@tooluniverse
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```
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Installs MCP server + 115 skills + slash commands in one step. Then see the
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`tooluniverse-claude-code-plugin` skill's "Recommended: turn on auto-update"
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step so future releases apply without manual `claude plugin update`.
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### Manual config (fallback)
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Make sure Step 2 is done (`uv --version` works).
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**Config file help** (if user seems unfamiliar): Config files are plain text that store settings — like a preference list for the app. You don't need to understand the format; just paste exactly what's shown below. Most apps have a Settings button that opens the file for you (see table). If the file is empty, paste the entire block. If it already has content, the agent should help merge it.
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@@ -149,14 +191,23 @@ Make sure Step 2 is done (`uv --version` works).
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}
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```
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**Config file locations:**
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> **Claude Code users**: skip manual MCP config — use the plugin instead. Invoke the `tooluniverse-claude-code-plugin` skill or run:
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> **Paste safely.** Copy the block whole — do not retype it. If the file already
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> has an `mcpServers` block, add only the `"tooluniverse": { ... }` entry inside
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> it and put a comma after the previous entry. If the file was empty, paste the
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> whole block. Then validate before restarting the app:
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> ```bash
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> claude plugin marketplace add mims-harvard/ToolUniverse
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> claude plugin install tooluniverse@tooluniverse
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> python3 -m json.tool < "<path-to-config>" > /dev/null && echo "JSON OK"
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> ```
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> This installs MCP server + 115 skills + slash commands in one step.
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> A trailing comma after the last entry, or a missing one between entries, is
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> the usual cause of "MCP server won't start".
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**`args` — `["tooluniverse"]` vs `["--refresh", "tooluniverse"]`**: plain is the
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default and starts fast from `uv`'s cache, but can stay on a cached older
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release until you run `uv cache clean tooluniverse`. Adding `--refresh` checks
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PyPI for the newest version on every launch — always current, a few seconds
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slower to start. Use plain unless the user specifically wants auto-updates.
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**Config file locations:**
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| Client | File | How to Access |
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|--------|------|---------------|
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@@ -302,7 +353,7 @@ Skills activate automatically based on user's question. Try: "Research the drug
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> tu info PubMed_search_articles # Check parameters
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> tu run PubMed_search_articles '{"query": "CRISPR cancer", "max_results": 3}'
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> tu run UniProt_get_entry_by_accession '{"accession": "P12345"}'
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> tu run FAERS_count_death_related_by_drug '{"drug_name": "metformin"}'
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> tu run FAERS_count_death_related_by_drug '{"medicinalproduct": "metformin"}'
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> ```
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## Write Agent Memory
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@@ -352,14 +403,26 @@ NVIDIA_API_KEY=your_shared_key
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| Issue | Fix |
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|-------|-----|
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| `error: externally-managed-environment` (PEP 668) | System `pip` refuses to install. Use `uv` — `uv venv --python 3.12 && source .venv/bin/activate && uv pip install tooluniverse`. Never `sudo pip` or `--break-system-packages`. |
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| `python3 -m venv` fails at `ensurepip` | Homebrew Python (3.13/3.14) is missing a working `ensurepip`. Use `uv venv --python 3.12` — `uv` supplies its own Python. |
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| `uv pip install` → "No virtual environment found" | Run `uv venv` first, or use `uv tool install tooluniverse` for just the `tu` command. |
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| `requires-python >= 3.10` | `uv python install 3.12` |
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| `uvx: command not found` | Run install script from Step 2, restart terminal |
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| Context window overflow | Verify using `uvx tooluniverse` (compact mode is default) |
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| `ModuleNotFoundError` | `uv pip install tooluniverse[all]` |
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| MCP server won't start | Test: `uvx tooluniverse` in terminal. Check JSON syntax. |
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| `ModuleNotFoundError` at tool runtime | An optional extra is missing. Run `tooluniverse-doctor` to see which group, then `uv pip install 'tooluniverse[ml]'` (or `[visualization]`, `[bioinformatics]`, `[all]`). |
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| Tools listed but fail when run | Normal for extras-backed tools — `tu status` counts loaded configs, not installed dependencies. `tooluniverse-doctor` reports which groups are missing. |
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| MCP server won't start | Test: `uvx tooluniverse` in terminal. Validate config with `python3 -m json.tool < <config>`. |
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| API key 401/403 | Check key in `env` block, restart app, verify key name |
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| Upgrade needed | `uv cache clean tooluniverse` then restart app |
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**Health check**: `tooluniverse-doctor` reports tools that failed to load *and*
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which optional dependency groups are not installed. Use it first whenever a tool
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errors unexpectedly.
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**`[all]` is not everything**: it covers `dev, docs, graph, visualization,
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space, embedding, ml, bioinformatics`. `singlecell`, `smolagents`, `client`,
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and `build` must be installed by name.
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Still stuck? [GitHub issues](https://github.com/mims-harvard/ToolUniverse/issues) or email [Shanghua Gao](mailto:[email protected]).
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## Quick Reference
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+23
-3
@@ -1,8 +1,8 @@
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---
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lineage_type: import
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upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/tooluniverse-admet-prediction/SKILL.md
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upstream_sha: e2520a96
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imported_at: 2026-06-26
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upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/089eb8e6/skills/tooluniverse-admet-prediction/SKILL.md
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upstream_sha: 089eb8e6
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imported_at: 2026-07-25
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prompt_class: unknown
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upstream_changes: accepted
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name: tooluniverse-admet-prediction
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@@ -33,6 +33,26 @@ Comprehensive pharmacokinetic and toxicity profiling integrating AI-based ADMET
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**Input**: Drug name (e.g., "ibuprofen") OR SMILES string (e.g., "CC(C)Cc1ccc(cc1)C(C)C(=O)O")
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## Before You Run
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ADMETAI tools run a local model, so they need the `ml` extra:
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```bash
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uv pip install 'tooluniverse[ml]'
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```
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Without it the tools still appear in `tu list` (the config loads) but fail at
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call time with `ADMETModel requires 'admet-ai' package`. Run
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`tooluniverse-doctor` to confirm which optional groups are installed.
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**Expected console noise — not errors.** The first ADMETAI call loads PyTorch
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and prints warnings such as missing-GPU / `Trainer` messages from
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PyTorch Lightning, and `TypedStorage is deprecated` from PyTorch. These are
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emitted by the underlying libraries during normal CPU inference. Predictions
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are unaffected — do not report them to the user as failures and do not retry
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the call because of them. Only treat output as a failure if the tool returns an
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`error` field or no predictions.
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---
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## COMPUTE, DON'T DESCRIBE
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-115
@@ -1,115 +0,0 @@
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---
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lineage_type: import
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upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/beea85fa/skills/tooluniverse-antigravity-plugin/SKILL.md
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upstream_sha: beea85fa
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imported_at: 2026-07-21
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prompt_class: unknown
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upstream_changes: accepted
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name: tooluniverse-antigravity-plugin
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description: Install, set up, verify, update, pin, uninstall, or troubleshoot the ToolUniverse plugin on Google Antigravity (AGY / Antigravity IDE / Antigravity 2.0). ALWAYS consult this skill for any of those — don't answer from memory, because the exact CLI name (agy), the "agy plugin install <path>" flow, the uvx tooluniverse MCP server, and the API-key env vars are easy to get wrong. Use it whenever someone wants to get ToolUniverse (or "the 1000+ scientific tools" / "the harvard tools") working on Antigravity, says the Antigravity plugin or its tools/skills won't load, hits a uvx or MCP-server startup error, asks how Antigravity updates it, wants to pin or remove it, or finds it running an old tool version. Not for the Codex plugin (use tooluniverse-codex-plugin) or Claude Code plugin (use tooluniverse-claude-code-plugin), for running research with the tools, or for authoring new tools or skills.
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disable-model-invocation: true
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---
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# Install the ToolUniverse Plugin for Google Antigravity (AGY)
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One-step install on Google Antigravity (AGY / Antigravity IDE / Antigravity 2.0): an MCP server exposing 1000+ scientific tools plus 120+ research skills — all auto-configured.
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## Prerequisites (check once)
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```bash
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uv --version # provides `uvx`; if missing: curl -LsSf https://astral.sh/uv/install.sh | sh
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agy --version # Antigravity CLI; if missing: https://antigravity.google
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```
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## Install
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In Antigravity, plugins can be installed using the `agy` CLI:
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### Option 1: Direct path / imported plugin install (recommended)
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```bash
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# If installed via Claude Code / Codex marketplace cache or cloned repo:
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agy plugin install /path/to/ToolUniverse/plugin
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```
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### Option 2: Clone + install
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```bash
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git clone https://github.com/mims-harvard/ToolUniverse.git
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cd ToolUniverse
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agy plugin install ./plugin
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```
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Restart Antigravity. The MCP server auto-starts via `uvx tooluniverse` on first use (~30 s cold start while the package downloads, instant after).
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## Verify it worked
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```bash
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agy plugin list
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```
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Expect output showing `tooluniverse` under `imports`:
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```json
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{
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"imports": [
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{
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"name": "tooluniverse",
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"source": "claude-code",
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"components": [
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"skills",
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"agents",
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"mcpServers",
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"hooks",
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"commands"
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]
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}
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]
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}
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```
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Inside Antigravity, just ask naturally:
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```
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What are the top mutated genes in breast cancer?
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Research the drug metformin.
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```
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The research skills auto-activate on matching questions, and the MCP tools are discovered and run via `find_tools` → `execute_tool` — no command prefix needed.
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## What you get
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| Component | What it does | How it's used |
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|---|---|---|
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| **MCP server** | 1000+ tools via `find_tools`, `get_tool_info`, `execute_tool` | Auto-loaded; no action needed |
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| **120+ skills** | Structured research workflows (drug discovery, variant interpretation, pharmacovigilance, phylogenetics, statistical modeling, etc.) | Auto-activate on matching questions |
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| **Research agent** | Autonomous multi-database research subagent | Auto-routed on complex research tasks |
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## API keys (optional, but recommended)
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Most tools work without keys. For higher rate limits or gated databases, set the keys you care about in `~/.gemini/config/plugins/tooluniverse/mcp_config.json` or pass them in environment variables:
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```bash
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export NCBI_API_KEY="your_key"
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export ONCOKB_API_TOKEN="your_token"
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export SEMANTIC_SCHOLAR_API_KEY="your_key"
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```
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## Update
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```bash
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uv cache clean tooluniverse
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```
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Restart Antigravity.
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## Troubleshooting
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| Symptom | Fix |
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|---|---|
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| `uvx: command not found` | Install `uv` (see Prerequisites), reopen terminal. |
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| MCP server won't start | Run `uv cache clean tooluniverse` or `uvx --refresh tooluniverse --help` in terminal. |
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| Plugin installs but tools missing | Restart Antigravity CLI/IDE. First launch downloads the package (~30 s). |
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| `requires-python >= 3.10` | `uv python install 3.12` |
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Still stuck: https://github.com/mims-harvard/ToolUniverse/issues
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Reference in New Issue
Block a user