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Setup on macOS

Target: Mac users (Apple Silicon or Intel) who have never installed Python or R before.

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 — Install Homebrew (the Mac package manager)

Open Terminal (Cmd+Space → type "Terminal" → Enter), then paste:

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

You'll be asked for your Mac password (it won't show as you type — that's normal). After ~5 minutes, Homebrew prints "Installation successful!"

Apple Silicon users (M1/M2/M3/M4): at the end of the install, Homebrew shows two echo commands to add Homebrew to your PATH. Run them, otherwise the brew command won't be found in new Terminal windows.

Verify:

brew --version

Expected: Homebrew 4.x.x

Step 2 — Install Python (via pyenv, recommended)

Why pyenv instead of system Python: macOS ships with an old Python 2 that confuses many tools. pyenv lets you install a clean Python 3.11 alongside it without breaking the system.

brew install pyenv
echo 'export PYENV_ROOT="$HOME/.pyenv"' >> ~/.zshrc
echo '[[ -d $PYENV_ROOT/bin ]] && export PATH="$PYENV_ROOT/bin:$PATH"' >> ~/.zshrc
echo 'eval "$(pyenv init -)"' >> ~/.zshrc
exec zsh
pyenv install 3.11.9
pyenv global 3.11.9

Verify:

python3 --version

Expected: Python 3.11.9

Faster alternative (if you don't need to manage multiple Python versions): brew install python@3.11 then symlink python3 to it. Less robust long-term but works.

Step 3 — Install R

brew install --cask r

The --cask flag installs the official R from CRAN (with the GUI). Takes about 5 minutes.

Verify:

Rscript --version

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

Recommended GUI: Install RStudio for a nicer experience.

brew install --cask rstudio

Step 4 — Install Node.js (for MCP servers)

brew install node@20

Verify:

node --version

Expected: v20.x.x

Step 5 — Install Git

Usually already installed on Mac. Verify:

git --version

If missing:

brew install git

Step 6 — Install Claude Code

Two options:

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

Option B — CLI (if you prefer Terminal):

brew install --cask claude

Verify:

claude --version

After install, run claude once and follow the login prompt (opens browser → log in to your Anthropic account).

Step 7 — Install Zotero + Better BibTeX

  1. Download Zotero from https://www.zotero.org/download/ and install.
  2. Open Zotero → 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 8 — Verify Everything

In Claude Code, run:

/setup-medsci

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

Step 9 — Install MedSci Skills

git clone https://github.com/Aperivue/medsci-skills.git ~/medsci-skills
cd ~/medsci-skills
open installers/install-macos.command

The .command file is a double-clickable installer that copies the skills into ~/.claude/skills/ and prompts you for confirmations.

Step 10 — Add MCP Servers (Optional)

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

You're Done

Try Demo 1:

cd ~/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.