alliance-plugins

Alliance of Genome Resources - Claude Code Resources

Shared Claude Code configurations, plugins, and best practices for Alliance of Genome Resources developers.

[!IMPORTANT] Claude Code runs in a regular terminal, not in the Claude web UI. Alliance access is for the Claude Code command-line tool only. If the Claude website or Claude desktop chat app still shows a personal Free plan, that is expected. To use Alliance-provided Claude Code access, open a normal terminal window on your computer (for example Terminal, iTerm, Windows Terminal, or PowerShell) and run Claude Code there.

Table of Contents

• What is Claude Code?
• Getting Started
• Essential Tips
• Extending Claude Code
  • Plugins
  • MCP Servers
• Tips & Best Practices
• Advanced Usage
• Contributing

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What is Claude Code?

Claude Code is a command-line tool that brings Claude AI directly into your terminal. Instead of copying code back and forth from a chat window, Claude Code can:

• Read and edit files in your project directly
• Run commands like tests, builds, and git operations
• Understand your codebase by exploring files and dependencies
• Make changes across multiple files to implement features or fix bugs

You interact with it through natural conversation in your terminal:

You:    Can you add error handling to the API client?
Claude: I'll add try/catch blocks and proper error messages. Let me read the current
        implementation first...
        [Claude reads files, makes edits, runs tests]

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Getting Started

Step 1: Request Access to the Alliance Anthropic Group

To get started with Claude Code at the Alliance, you need to be added to our Anthropic organization:

1. Message Chris T on the Alliance Slack
2. Include in your message:
   • A request to be added to the Alliance Anthropic group
   • The email address you want to use for your Claude account

You'll receive an email invitation to join the Alliance Anthropic organization once your request is processed.

Step 2: Read the Official Quickstart

⚠️ Please take 10 minutes to read this: Claude Code Quickstart Guide

The official guide covers essential workflows that will save you hours:

• How to ask Claude effective questions
• Git integration (commits, branches, merge conflicts)
• Debugging and feature implementation patterns
• Pro tips that make a real difference

You'll get far more out of Claude Code if you understand its capabilities upfront.

Step 3: Install Claude Code

As mentioned in the quickstart guide, once you've received your invitation and created your account, install the Claude Code CLI:

macOS, Linux, WSL:

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

Windows PowerShell:

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

Alternative: Homebrew (macOS/Linux):

brew install --cask claude-code

One-time installation: Claude Code only needs to be installed once per computer. After installation, you can run claude from any directory - you don't need to install it separately for each project or repository.

Note: Native installations auto-update automatically. Homebrew requires manual updates via brew upgrade claude-code.

Step 4: Log In and Start Using Claude Code

1. Open your terminal in any project directory
2. Start Claude Code:

   claude
   

3. Log in when prompted:
   • Use the email you provided in Step 1
   • Important: When asked to choose an account type, select the second option: "Anthropic Console Account" (API Usage Billing). Don't select the first option (Claude Pro/Max subscription).
4. Start coding! Try asking:

   > what does this project do?
   

Step 5: Set Your Model to Opus

⚠️ Important: Make sure your model is set to Opus for the best results.

Check and set your model:

/model

Select Opus from the list. This setting persists across sessions.

Why Opus? Opus is Claude's most capable model - it handles complex codebases better, makes fewer mistakes, and produces higher quality code. If you're finding Claude's suggestions unhelpful or off-target, check that you're using Opus.

Additional Resources

• CLI Reference - All commands and options
• Common Workflows - Step-by-step guides

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Essential Tips

These three habits will dramatically improve your experience with Claude Code. They're simple but make a huge difference in the quality and reliability of the code Claude produces.

1. Make a Plan Before Coding