Setup medsci
Agent Skills for medical research — literature search, reporting-guideline & citation checks, statistics, publication figures, submission. Works with Claude Code, Codex, Cursor & GitHub Copilot. Built by a physician-researcher, tested on real publications. MIT.
npx -y skills add Aperivue/medsci-skills --skill setup-medsciAssembled from the repository path, not quoted from the project. Check it against their README if it does not work.
What its author says it does
Copied from the file, not written here
Diagnostic checklist for the MedSci Skills runtime. Verifies Python, R, Node, Claude Code, Git, Zotero, and configured MCP servers, and prints a pass/fail table with links to the right setup doc for any missing component. Read-only — does not install anything.
SKILL.md
5.8 KB, as published. Nobody here has run it
Setup-MedSci Skill
You are helping a medical researcher verify that their environment is correctly configured to run MedSci Skills. You do not install anything — you only diagnose what's present, what's missing, and where to find the setup doc for any missing component. This skill is intentionally read-only so that a doctor can run it safely without worrying about breaking their system.
Communication Rules
- Communicate with the user in their preferred language (Korean or English).
- The diagnostic table itself is in English so it can be pasted into GitHub issues for support.
- All recommended remediation links point to
docs/setup/markdown guides in the medsci-skills repo.
Workflow
Phase 1: Detect OS
Run:
uname -s
Darwin→ macOS path → recommenddocs/setup/mac.mdLinux→ Linux path (uses similar tooling to Mac) → recommenddocs/setup/mac.mdMINGW*,MSYS*,CYGWIN*, or detection failure on Windows → recommenddocs/setup/windows.md
Phase 2: Run Diagnostic Commands
For each tool, run the command and capture both the version output and the exit code:
| Tool | Command | Required version |
|---|---|---|
| Python | python3 --version (Mac/Linux) or python --version (Windows) | 3.11 or higher |
| R | Rscript --version (writes to stderr) | 4.0 or higher |
| Node.js | node --version | v20 or higher |
| Git | git --version | 2.30 or higher |
| Claude Code CLI | claude --version | any |
| MCP servers | claude mcp list | at least one of: zotero, gdrive, pubmed, filesystem |
Use command -v <tool> first to detect presence without running it (avoids triggering long initialization).
Phase 3: Emit Checklist Table
Print a single Markdown table to stdout in this exact format:
## MedSci Skills Setup Diagnostic
OS detected: <macOS | Linux | Windows>
Date: <YYYY-MM-DD>
| Component | Status | Detected | Required | Action |
|---|:---:|---|---|---|
| Python 3.11+ | ✅ / ❌ | 3.11.9 | 3.11+ | OK / See docs/setup/mac.md Step 2 |
| R 4.x | ✅ / ❌ | 4.3.1 | 4.0+ | OK / See docs/setup/mac.md Step 3 |
| Node.js 20+ | ✅ / ❌ | v20.11.1 | v20+ | OK / See docs/setup/mac.md Step 4 |
| Git | ✅ / ❌ | 2.42.0 | 2.30+ | OK / See docs/setup/<os>.md Step 5 |
| Claude Code CLI | ✅ / ❌ | 1.5.x | any | OK / See docs/setup/<os>.md Step 6 |
| MCP: zotero | ✅ / ❌ / ⚠️ | Connected | optional | OK / See docs/setup/mcp-setup.md |
| MCP: gdrive | ✅ / ❌ / ⚠️ | Connected | optional | OK / See docs/setup/mcp-setup.md |
| MCP: filesystem | ✅ / ❌ | Connected | recommended | OK / See docs/setup/mcp-setup.md |
Summary: <X required components passed, Y missing>
Next step: <one-sentence action>
Status legend:
- ✅ Present and meets minimum version
- ❌ Missing or below minimum version
- ⚠️ Present but optional and not connected
Phase 4: Suggest Remediation
If everything ✅: "Your environment is ready. Try Demo 1 with cd ~/medsci-skills/demo/01_wisconsin_bc && claude '/orchestrate --e2e'."
If anything ❌ in required rows: print the corresponding doc link. Do not offer to install — direct the user to follow the doc step. The doc tells them exactly what to copy-paste.
If only optional MCP rows are ❌: explain that MedSci Skills work without MCP servers but lit-sync, verify-refs, and write-paper are smoother with Zotero MCP. Offer the docs/setup/mcp-setup.md link.
Reference Files
references/setup-checklist.md— verbatim list of every check this skill runs and the corresponding documentation link
Output Contract
| Artifact | Filename | Format |
|---|---|---|
| Diagnostic report | stdout (Markdown table) | Markdown |
| Optional log | ~/.medsci-skills/diagnostic-YYYY-MM-DD.md | Markdown |
If the user asks for a copyable report (e.g., for a GitHub issue), write the diagnostic to the optional log path and tell them where it is.
What This Skill Does NOT Do
- Does not install anything. No
brew install,winget install,pip install,Rscript -e 'install.packages(...)', or any other state-changing command. Read-only diagnostics only. - Does not modify
~/.claude.jsonor any MCP configuration. It only readsclaude mcp listoutput. - Does not check skill versions or skill content. That is the job of
validate_skills.shandmanage-project status. - Does not auto-fix anything. If a tool is missing, the user must go to the setup doc and follow the steps themselves. This is intentional — auto-installers for system Python and R are a support nightmare for non-developer users.
Anti-Hallucination
- Never fabricate version numbers. Always run the actual command and report the exact stdout. If the command fails, report the failure verbatim — do not guess what version is "probably" installed.
- Never invent doc paths. The five setup docs are:
docs/setup/README.md,docs/setup/mac.md,docs/setup/windows.md,docs/setup/mcp-setup.md,docs/setup/common-issues.md. Do not link to a doc that does not exist in the repo. - Never claim an MCP server works without verifying via
claude mcp list. A configured-but-disconnected server is ⚠️, not ✅. - If
command -vreports a tool present but the version flag fails, mark the row ❌ and report the failure command — the install is broken, not just outdated.