This guide walks you through setting up Claude Code and the Reactome curator workflow skills on a Mac, starting from scratch. No prior experience with the Terminal is assumed.
Time to complete: approximately 20–30 minutes (first time only).
| Component | What it is |
|---|---|
| Terminal | The text-based window where you type commands to control your Mac |
| Git | A tool that downloads and updates code from GitHub |
| Node.js | A software platform required by Claude Code |
| Claude Code | The AI assistant that runs in your Terminal |
| reactome-curator-workflows | The Reactome skill library — curation tools powered by Claude Code |
| Python 3 + packages | Required by two skills: /generate-doi-batch and /reactome-qa-tracker |
You need:
- A Mac running macOS Ventura (13) or later. To check: Apple menu → About This Mac.
- An Anthropic API key issued from the Reactome organizational account.
- Contact Marc Gillespie (gillespm@stjohns.edu) to receive your key.
- Log in at platform.anthropic.com → API Keys → Create Key.
- Copy it immediately — it looks like
sk-ant-api03-...and will not be shown again. - See the Reactome API Key Setup Guide for full instructions on obtaining and securing your key.
API key vs. Claude.ai Pro: The Reactome organizational API key bills against the shared AI for Science credit pool. Your personal Claude.ai Pro subscription (if you have one) is separate and unaffected. Always use the organizational key for Reactome pipeline work.
Terminal is a program already on your Mac. It lets you type commands instead of clicking buttons.
To open Terminal:
- Press
Command (⌘) + Spaceto open Spotlight Search. - Type Terminal and press
Return.
A window opens with a prompt that looks something like:
yourname@MacBook-Pro ~ %
The ~ symbol means you are in your Home folder. The % is where you type commands.
How to use this guide: When you see a command in a grey box, click anywhere in the box to select it, copy it (Command-C), paste it into Terminal (Command-V), and press Return to run it. Run one command at a time and wait for each to finish.
Code projects live by convention in a Developer folder in your Home folder. Run this command to create it:
mkdir -p ~/Developer
Nothing visible happens if it works — that is normal.
Check whether Git is already installed:
git --version
If you see a version number, Git is installed — skip to Step 4. If you see command not found, run:
xcode-select --install
A dialog will appear asking you to install the Command Line Tools. Click Install, then Agree. This takes a few minutes. When it finishes, run git --version again to confirm.
Set your Git identity (required for commits):
git config --global user.name "Your Name"
git config --global user.email "your@email.com"
Claude Code requires Node.js 18 or higher. Check whether it is already installed:
node --version
If you see v18.x.x or higher, skip to Step 5. If you see an older version or command not found, install Node.js using the official installer:
- Go to https://nodejs.org and download the LTS release. The site auto-detects whether you have Apple Silicon (M1/M2/M3/M4) or Intel and offers the correct package — you do not need to choose.
- Run the downloaded
.pkgfile and follow the prompts.
Verify after installation:
node --version
You should see v20.x.x or similar.
Claude Code is installed with a single command:
curl -fsSL https://claude.ai/install.sh | bash
Verify:
claude --version
You should see a version number like 1.x.x.
Add your Reactome organizational API key to your shell configuration so it is available every time you open Terminal. Replace your-key-here with the actual key you obtained in the Before You Start section above.
echo 'export ANTHROPIC_API_KEY="your-key-here"' >> ~/.zshrc
source ~/.zshrc
Verify the key is set:
echo $ANTHROPIC_API_KEY
You should see your key printed. If you see a blank line, repeat the two commands above and confirm you replaced your-key-here with the real key.
Authentication note: Claude Code offers two login methods — a Claude.ai subscription (OAuth, no per-token charges) and the Anthropic Console (API key, pay-as-you-go). For Reactome work, always use the API key method so usage bills to the shared organizational credit pool. When ANTHROPIC_API_KEY is set in your environment, it takes priority automatically. Run /status inside Claude Code at any time to confirm which credentials are active.
Security: Your key is stored only on your local Mac in ~/.zshrc. Never commit it to GitHub or share it in Slack or email.
Quick verification — confirm the key is active and billing to the Reactome account:
curl https://api.anthropic.com/v1/messages \
-H "x-api-key: $ANTHROPIC_API_KEY" \
-H "anthropic-version: 2023-06-01" \
-H "content-type: application/json" \
-d '{"model": "claude-haiku-4-5-20251001", "max_tokens": 32,
"messages": \[{"role": "user", "content": "Hello"}\]}'
A JSON response containing "type": "message" confirms your key is working.
Before cloning, Marc must add you as a collaborator on GitHub. You will receive an email invitation — accept it before running this command.
git clone https://github.com/reactome/reactome-curator-workflows.git \
\~/Developer/reactome-curator-workflows
If prompted for a password: use a personal access token, not your GitHub account password. Generate one at https://github.com/settings/tokens with the repo scope selected. Paste the token where Terminal asks for your password.
Navigate into the folder:
cd ~/Developer/reactome-curator-workflows
Confirm you are in the right place:
ls
You should see files including CLAUDE.md, README.md, and a .claude/ directory.
Two skills (/generate-doi-batch and /reactome-qa-tracker) require Python 3 and two packages. Python 3 is already on modern Macs. Install the packages:
pip3 install pandas openpyxl
If you see a permissions error, try:
pip3 install --user pandas openpyxl
If you see a PATH warning after installing, add the path to your shell config (replace 3.x with the version number shown in the warning):
echo 'export PATH="/Users/[you]/Library/Python/3.x/bin:$PATH"' >> ~/.zshrc
source ~/.zshrc
Every time you want to use the Reactome skills, open Terminal and run:
cd ~/Developer/reactome-curator-workflows
claude
The first line moves you into the Reactome repo folder. The second starts Claude Code, which automatically reads CLAUDE.md and loads all skills. You will see a welcome message and a prompt where you can start typing.
To confirm everything loaded correctly, ask Claude:
"What do you know about this project?"
Claude should describe Reactome, the team, and the available skills.
Important: Always launch Claude Code from inside the reactome-curator-workflows folder, not from another directory. Some skills (particularly /extract-reactions) rely on .claude/settings.json in the repo root for domain allowlisting.
Mac app note: The Claude for Mac desktop app's </> Claude Code button runs in a cloud/OAuth-only context and does not read ANTHROPIC_API_KEY from your shell. Always launch Claude Code from Terminal for Reactome work.
Type a skill name at the Claude Code prompt to invoke it. For example:
/internal-module-review
Claude Code will guide you through the required inputs. See the Reactome Curator Workflows — Claude Code Usage Guide (in this repository) for full documentation on each skill.
New skills and updates are published to GitHub. Pull the latest version before each session:
cd ~/Developer/reactome-curator-workflows
git pull
New or updated skills are available immediately after pulling — no restart of Claude Code is needed if it is already running.
| What you want to do | Command |
|---|---|
| Open Terminal | Command (⌘) + Space, type "Terminal", press Return |
| Go to the Reactome repo | cd ~/Developer/reactome-curator-workflows |
| Start Claude Code | claude |
| Check active credentials | /status (inside Claude Code) |
| Check session token usage | /cost (inside Claude Code) |
| Update the repo | git pull |
| Exit Claude Code | Type /exit or press Control-C |
claude: command not found Claude Code is not on your PATH. Close Terminal, reopen it, and try again. If the problem persists, run curl -fsSL https://claude.ai/install.sh | bash again.
Error: Invalid API key Your key is not set or is incorrect. Run echo $ANTHROPIC_API_KEY to check. If blank, repeat Step 6. Confirm the key in ~/.zshrc has no extra spaces or quotation marks inside the key itself.
Claude Code uses my Claude.ai account instead of the API key Check that ANTHROPIC_API_KEY is exported: echo $ANTHROPIC_API_KEY. If blank, the variable is not set. Run /status inside Claude Code to confirm the active authentication method.
git: command not found Git is not installed. Repeat Step 3.
Python package import errors when running a skill Run pip3 install pandas openpyxl again. If you get a permissions error, use pip3 install --user pandas openpyxl.
GitHub prompts for a password during clone Use a personal access token, not your GitHub password. See Step 7.
PMID resolution returns blanks in /extract-reactions Make sure you launched Claude Code from inside the reactome-curator-workflows folder (Step 9), not from another directory.
~/Developer/reactome-curator-workflows/
├── CLAUDE.md ← project context (read automatically by Claude Code)
├── README.md ← skill documentation and prerequisites table
├── MacOS_Setup_Guide.md ← this file
├── Reactome_CuratorWorkflows_ClaudeCode_Guide_v2.docx ← skill usage guide
├── Reactome_API_Key_Setup.docx ← API key setup and credit management
├── .gitignore
├── chrome-extensions/
│ └── pmid-tagger/ ← Chrome extension: prefix downloads with PMID-<id>_
└── .claude/
├── settings.json ← host allowlist (eutils.ncbi.nlm.nih.gov, etc.)
└── skills/
├── internal-module-review/ ← /internal-module-review
├── annotate-pathway-from-reviews-or-topic\_name/ ← /annotate-pathway-from-reviews-or-topic\_name
├── extract-reactions/ ← /extract-reactions
├── generate-doi-batch/ ← /generate-doi-batch
├── update-gdrive-readme/ ← /update-gdrive-readme
├── reactome-qa-tracker/ ← /reactome-qa-tracker
└── reactome-neo4j-ols-setup/ ← /reactome-neo4j-ols-setup
- Repo maintainer: Marc Gillespie (NYU / SJU) — gillespm@stjohns.edu
- Curation standards questions: Reactome curator Slack channel
- Repo or skill questions: open a GitHub issue at https://github.com/reactome/reactome-curator-workflows/issues