Set up a terminal AI agent before Friday.

In 3.2 you build a knowledge base with an AI agent that works on files on your own computer, so it will not run in Claude or ChatGPT in a web browser. Do this page before class: install Claude Code or Codex CLI in the terminal, and check that it answers. Paperclip, a literature search tool, is optional. It takes about 20 minutes.

Stuck? Email biocore@umassmed.edu macOS or Windows · Your own computer, with permission to install software

Set up

If anything below fails to install, or your computer does not let you install software, contact us at biocore@umassmed.edu before Friday. We would rather sort it out this week than in class.

Can’t install, or no paid subscription? Come anyway. John does every step of the exercise live on the projector, so you can follow along and watch what the agent does.

Check what you need

A paid Claude or ChatGPT subscription. Free plans do not include these agents.
One terminal AI agent, your choice: Claude Code (with a Claude plan) or Codex CLI (with a ChatGPT plan). The next step installs it.

Never used a terminal? That is fine, and part of the point of the session: you paste one line to install, type one word to start, and from then on you talk to the agent in plain English.

Open a terminal

macOS: press Cmd+Space, type Terminal, and press Enter.

Windows: click Start, type PowerShell, and press Enter.

Paste each command below into the terminal and press Enter.

Install Claude Code or Codex CLI

You only need one of the two.

Claude Code, macOS:

curl -fsSL https://claude.ai/install.sh | bash

Claude Code, Windows PowerShell:

irm https://claude.ai/install.ps1 | iex

Codex CLI, macOS:

curl -fsSL https://chatgpt.com/codex/install.sh | sh

Codex CLI, Windows PowerShell:

powershell -ExecutionPolicy ByPass -c "irm https://chatgpt.com/codex/install.ps1 | iex"

Then start it: type claude for Claude Code or codex for Codex CLI, press Enter, and follow the login instructions.

Check that it works

With your agent started, type:

What can I do with coding agents?

Checkpoint The agent answers in the terminal. If it does, you are ready for Friday. Type /exit (Claude Code) or press Ctrl+C twice to leave.

Only if the terminal will not work: a desktop app

The terminal agents are what the exercise is built and tested for. The desktop apps are a fallback: you will very likely run into trouble with some of the exercise steps in them. Use one only if you cannot get Claude Code or Codex CLI to run, and expect to watch John for the steps that misbehave.

FALLBACK Claude desktop app (Code tab)

Download Claude for macOS or Windows from claude.com/download, install it, open it, and sign in.
Click the Code tab at the top, choose Local, and click Select folder. If it asks you to upgrade, your account is not on a paid plan yet.
Windows only: the Code tab needs Git for Windows. Install it with the default options, then restart Claude.

FALLBACK ChatGPT desktop app

Download the ChatGPT desktop app from OpenAI’s app page, install it, open it, and sign in. On a Mac it needs Apple Silicon (M1 or newer).
Check that you can open a folder on your computer as a project.

Account through your lab? Check with your PI

If your Claude seat comes from a lab or department plan (a Claude Team plan, including Anthropic’s Team plan for scientists, or Enterprise), Claude Code may be switched off until an Owner, usually the PI, allows it. A personal Pro or Max plan needs none of this.

Claude Code: if it will not let you sign in, or says your plan does not include it, the PI should check the Claude Code admin settings and make sure your seat includes Claude Code.
ChatGPT through a lab or school workspace: ask your workspace admin to confirm that Codex is allowed for your account.

Optional: install Paperclip for literature search

Paperclip is a scientific paper index that gives your agent search and retrieval over more than 8 million papers. It makes the literature steps in 3.2 better, but you do not need it: without it, your agent searches PubMed Central through NCBI instead, with no install and no account.

First create a free Paperclip account. Then open a terminal (on macOS, Terminal; on Windows, PowerShell) and install it.

macOS:

curl -fsSL https://paperclip.gxl.ai/install.sh | bash

Windows: Paperclip has no Windows installer yet, so install it with Python.

If you do not have Python, install it from python.org. On the installer’s first screen, tick Add python.exe to PATH. Then close PowerShell and open a new one.
Paste these three lines into PowerShell:

Invoke-WebRequest https://paperclip.gxl.ai/paperclip.whl -OutFile "$env:TEMP\gxl_paperclip-0-py3-none-any.whl"
python -m pip install --no-deps "$env:TEMP\gxl_paperclip-0-py3-none-any.whl"
python -m pip install requests click pyyaml

Close PowerShell and open a new one, so it finds the new paperclip command.

WHY Why three lines instead of one?

The download is a standard Python package, but its file name is too short for Python’s installer to accept, so the first line saves it under a name it will take. The second line installs Paperclip, and the third installs the three packages it needs. This is the same thing the macOS installer does.

Both: set Paperclip up for your agent. It asks you to sign in with the account you just made.

paperclip install

Checkpoint paperclip config shows your email next to Auth. If Paperclip will not install, skip it and let us know at biocore@umassmed.edu; each step in 3.2 that uses it shows an NCBI prompt to use instead.