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Setup on Windows

Target: Windows 10/11 users who have never installed Python or R before. WSL (Windows Subsystem for Linux) is not required — everything works natively on Windows.

If you already have some of these installed, the diagnostic skill (/setup-medsci from inside Claude Code) will tell you what to skip.

Step 1 — Open PowerShell as Administrator

  1. Press Windows key, type "PowerShell".
  2. Right-click Windows PowerShell → Run as Administrator.

Most installers below need admin rights.

Step 2 — Install winget (the Windows package manager)

winget is built into Windows 11 and recent Windows 10. Verify:

winget --version

If missing, install App Installer from the Microsoft Store (https://www.microsoft.com/store/productId/9NBLGGH4NNS1).

Step 3 — Install Python 3.11

winget install --id Python.Python.3.11 -e

Important: After install, close PowerShell and reopen it (so the PATH refreshes).

Verify:

python --version

Expected: Python 3.11.x

If you see Python 2.x.x or "command not found", see common-issues.md → "Windows Python PATH".

Step 4 — Install R

winget install --id RProject.R -e

Verify (after closing/reopening PowerShell):

Rscript --version

Expected: R scripting front-end version 4.x.x

Recommended GUI: RStudio.

winget install --id Posit.RStudio -e

Step 5 — Install Node.js 20

winget install --id OpenJS.NodeJS -e

Verify (close/reopen PowerShell):

node --version

Expected: v20.x.x

Step 6 — Install Git

winget install --id Git.Git -e

Verify:

git --version

Step 7 — Install Claude Code

Option A — Desktop app (easiest): Download from https://claude.ai/download and install.

Option B — Via winget (if available):

winget install --id Anthropic.Claude -e

Verify:

claude --version

After install, run claude once → it opens your browser to log in to your Anthropic account.

Step 8 — Install Zotero + Better BibTeX

  1. Download Zotero from https://www.zotero.org/download/ and install.
  2. Open Zotero → Edit → Preferences → Sync → log in.
  3. Install Better BibTeX: download .xpi from https://github.com/retorquere/zotero-better-bibtex/releases/latest → in Zotero, Tools → Add-ons → gear icon → Install Add-on From File → select the downloaded .xpi.
  4. Restart Zotero.

Step 9 — Verify Everything

In Claude Code, run:

/setup-medsci

You should see a checklist with all green ✅ marks. If anything is ❌, the checklist tells you which step to revisit.

Step 10 — Install MedSci Skills

cd $HOME
git clone https://github.com/Aperivue/medsci-skills.git
cd medsci-skills
.\installers\install-windows.cmd

Or double-click install-windows.cmd in File Explorer (Allow → Yes when SmartScreen warns; the script is open-source and viewable in the repo).

Step 11 — Add MCP Servers (Optional)

See mcp-setup.md for Zotero, Google Drive, and PubMed MCP integration.

You're Done

Try Demo 1:

cd $HOME\medsci-skills\demo\01_wisconsin_bc

Then in Claude Code: /orchestrate --e2e

Expected: a complete IMRAD manuscript + ROC curves + STARD compliance report in ~10 minutes.

Issues? See common-issues.md.

Common Windows Quirks

  • PowerShell vs Command Prompt: Use PowerShell. Most install commands assume PowerShell.
  • Antivirus warnings: Windows Defender or third-party AV may flag git, python, or claude installers as "unrecognized." This is normal for newly-released versions — click More info → Run anyway if the source is the official one above.
  • PATH after install: Always close and reopen PowerShell after installing a new tool, otherwise the new command isn't found yet.
  • OneDrive interference: If you cloned the repo into a OneDrive-synced folder (Documents, Desktop), some scripts may stall. Move the repo to C:\Users\YourName\medsci-skills instead.