plugin/skills/tooluniverse-install-skills/SKILL.md
Detect and auto-install missing ToolUniverse research skills. Checks common Claude Code/Cursor/Codex skill directories for the canary file, and installs any missing skills if none found. Use when the plugin's research skills aren't loading, when migrating between clients, or when verifying a skill installation.
npx skillsauth add mims-harvard/tooluniverse tooluniverse-install-skillsInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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Checks whether the ToolUniverse specialized skills are installed and installs them automatically if not.
Use the Shell tool to check for the canary file across all common client locations:
ls .cursor/skills/tooluniverse-drug-research/SKILL.md 2>/dev/null \
|| ls .agents/skills/tooluniverse-drug-research/SKILL.md 2>/dev/null \
|| ls .windsurf/skills/tooluniverse-drug-research/SKILL.md 2>/dev/null \
|| ls .gemini/skills/tooluniverse-drug-research/SKILL.md 2>/dev/null \
|| ls .claude/skills/tooluniverse-drug-research/SKILL.md 2>/dev/null \
|| ls .opencode/skills/tooluniverse-drug-research/SKILL.md 2>/dev/null \
|| ls .trae/skills/tooluniverse-drug-research/SKILL.md 2>/dev/null \
|| ls .skills/tooluniverse-drug-research/SKILL.md 2>/dev/null \
|| echo "NOT_INSTALLED"
NOT_INSTALLED → proceed to installation.# 1. Download skills from GitHub (shallow, sparse — only skills/ folder)
git clone --depth 1 --filter=blob:none --sparse \
https://github.com/mims-harvard/ToolUniverse.git /tmp/tu-skills
cd /tmp/tu-skills && git sparse-checkout set skills
# 2. Copy to the correct directory for the detected client:
mkdir -p .cursor/skills && cp -r /tmp/tu-skills/skills/* .cursor/skills/ # Cursor
# mkdir -p .agents/skills && cp -r /tmp/tu-skills/skills/* .agents/skills/ # Codex/OpenAI
# mkdir -p .windsurf/skills && cp -r /tmp/tu-skills/skills/* .windsurf/skills/ # Windsurf
# mkdir -p .gemini/skills && cp -r /tmp/tu-skills/skills/* .gemini/skills/ # Gemini CLI
# mkdir -p .claude/skills && cp -r /tmp/tu-skills/skills/* .claude/skills/ # Claude Code
# mkdir -p .opencode/skills && cp -r /tmp/tu-skills/skills/* .opencode/skills/ # OpenCode
# mkdir -p .trae/skills && cp -r /tmp/tu-skills/skills/* .trae/skills/ # Trae
# mkdir -p .skills && cp -r /tmp/tu-skills/skills/* .skills/ # Cline/VS Code
# 3. Clean up
rm -rf /tmp/tu-skills
If the client cannot be detected automatically, ask the user which one they use before running step 2.
Detect the client from the presence of config files:
| Config file present | Client |
|---|---|
| .cursor/ | Cursor |
| .agents/ | Codex / OpenAI |
| .windsurf/ | Windsurf |
| .gemini/ | Gemini CLI |
| .claude/ | Claude Code |
| .opencode/ | OpenCode |
| .trae/ | Trae |
| None of the above | Ask the user |
Confirm success:
ls .cursor/skills/tooluniverse-drug-research/SKILL.md
Tell the user: "ToolUniverse skills installed successfully. You now have access to 50+ specialized research workflows."
tools
Post-market safety surveillance and recall/adverse-event RETRIEVAL across the full spectrum of FDA-regulated products that are NOT covered by the drug-AE signal skills: medical devices, food / dietary supplements / cosmetics, veterinary drugs, and drug supply (shortages). Orchestrates openFDA endpoints (MAUDE device adverse events + device recalls + 510(k), CAERS food/supplement/ cosmetic adverse events, veterinary adverse events, drug shortages, and cross-product enforcement/recall reports). USE WHEN the user asks: "are there adverse events for [device / pacemaker / infusion pump / insulin pump]", "device recalls for [firm/product]", "supplement / vitamin / cosmetic adverse reactions", "is [drug] in shortage", "what injectables are on shortage", "veterinary / animal adverse events for [drug] in [dog/cat/horse]", "food recall for listeria", "MAUDE report for [device]", "CAERS reactions for [brand]". DO NOT USE for drug adverse-event SIGNAL detection or disproportionality (PRR / ROR / IC) or drug-AE association scoring — that is `tooluniverse-pharmacovigilance` / `tooluniverse-adverse-event-detection`. This skill is multi-product surveillance and retrieval, not drug-AE statistical signal mining.
tools
--- name: tooluniverse-phewas description: Cross-ancestry / cross-biobank phenome-wide association (PheWAS) and replication. Given ONE variant (rsID) or ONE gene, look up every phenotype it associates with across European/UK (UKB-TOPMed), Finnish (FinnGen), Japanese (BioBank Japan), and Taiwanese (TPMI) biobanks, plus exome-wide gene-burden PheWAS (Genebass), then judge whether an association replicates across ancestries or is population-specific. Use whenever the user asks "what else is this va
tools
Dereplicate a putative natural product and assign its chemical taxonomy. Use to answer "is [compound] a known natural product", "what microbe/organism produces [compound]", "what chemical class is [compound]", "dereplicate this metabolite (by formula/exact mass/InChIKey/SMILES)", or "classify this molecule into ChemOnt". Searches NPAtlas for known microbial natural products (producing organism + literature reference), assigns the ChemOnt kingdom→superclass→class→subclass hierarchy via ClassyFire, resolves systematic IUPAC names to structure via OPSIN, and cross-references identity in PubChem. NOT for general drug/compound identity or ADMET (use tooluniverse-chemical-compound-retrieval / tooluniverse-small-molecule-discovery) and NOT for metabolomics pathway/enrichment analysis (use tooluniverse-metabolomics skills).
tools
Genome-ASSEMBLY discovery, QC, and replicon mapping for any organism (bacteria, archaea, fungi, and beyond) using NCBI Datasets. Resolves an organism name or taxid to assemblies, picks the reference/representative or best-quality assembly, pulls assembly QC metrics (total length, contig/scaffold N50, contig count, GC%, assembly level, RefSeq category), enumerates chromosomes and plasmids via per-replicon sequence reports, and compares candidate assemblies on quality. Use for "what genomes are available for [organism]", "assembly stats / N50 / GC content for [GCF_/GCA_ accession]", "how many plasmids does [strain] have", "compare assemblies for [species]", "find the reference genome for [taxon]", "is this assembly Complete Genome or just contigs". NOT for gene-level orthology/synteny (use tooluniverse-comparative-genomics), plant gene structure (use tooluniverse-plant-genomics), de novo assembly from raw reads (no tool exists), or taxonomy-only name/lineage lookups.