Advanced Configuration

Customizing Claude Code for lab workflows

Claude Code / Advanced

Advanced 5 min read Phase 4: Advanced

← HPC Usage Next: Global Config →

Prerequisites

• Daily Workflow (comfortable with basic usage)

This section covers advanced Claude Code configuration for power users and lab-wide standardization.

Configuration Hierarchy

Claude Code reads configuration from multiple levels:

~/.claude/CLAUDE.md          # Global (all projects)
~/.claude/settings.json      # Global settings
    ↓
.claude/CLAUDE.md            # Project-specific
.claude/settings.json        # Project settings
.claude/commands/*.md        # Custom skills
.claude/agents/*.md          # Custom agents
    ↓
CLAUDE.md                    # Project root (legacy)

Lower levels override higher levels for conflicting settings.

Quick Setup

Copy Lab Templates

# Global config (do once)
mkdir -p ~/.claude
cp ~/rashid-lab-setup/lab-handbook/config/claude/student-CLAUDE.md ~/.claude/CLAUDE.md

# Project config (for each project)
mkdir -p .claude/commands .claude/agents

Recommended Plugins

claude plugins install github@claude-plugins-official
claude plugins install commit-commands@claude-plugins-official
claude plugins install superpowers@superpowers-marketplace
claude plugins install scientific-skills@claude-scientific-skills

Topics

Topic	Description
Global Config	User-level CLAUDE.md and settings
Skills	Custom /commands for common tasks
Agents	Specialized agents for complex work
Hooks	Automation triggers for events
MCP Servers	External tool integrations
Enforcing Standards	Lab-wide consistency

Lab-Provided Templates

The lab provides ready-to-use templates:

Global CLAUDE.md

Template	For
config/claude/student-CLAUDE.md	Lab members
config/claude/pi-CLAUDE.md	PI (includes admin section)

Project Templates

Each lab template repo includes .claude/ with: - CLAUDE.md — Project context - settings.json — Permissions - commands/review.md — /review skill - agents/lab-reviewer.md — Code review agent

What’s Possible

With advanced configuration, you can:

• Enforce standards — Claude follows lab conventions automatically
• Automate reviews — Code review runs after every session
• Custom workflows — /preflight checks before Slurm submission
• Integrate tools — Connect to databases, APIs, and lab systems
• Share knowledge — Team-wide agents that know lab practices

Getting Started

1. Start with Global Config to set up your personal settings
2. Add Skills for common project tasks
3. Configure Hooks for automation
4. Explore MCP Servers for external integrations