Global Configuration

User-level CLAUDE.md and settings

Modified

February 1, 2026

Advanced 8 min read Phase 4: Advanced

Global configuration applies to all projects and ensures Claude always knows your preferences.

~/.claude/CLAUDE.md

This file provides context that applies everywhere:

# My Claude Configuration

## Lab Organization
- Lab: Rashid Lab, Biostatistics, UNC Chapel Hill
- GitHub: https://github.com/rashidlab
- Team roster: ~/rashid-lab-setup/config/team.yml

## Coding Standards
- Data manipulation: Base R + data.table (NOT tidyverse)
- Pipelines: {targets}
- Communication: Microsoft Teams

## Common Commands
- Pipeline: Rscript -e "targets::tar_make()"
- Longleaf: ssh <onyen>@longleaf.unc.edu

## Resources
- Lab Handbook: https://rashidlab.github.io/lab-handbook/

Lab Templates

Copy the lab template to get started:

mkdir -p ~/.claude
cp ~/rashid-lab-setup/lab-handbook/config/claude/student-CLAUDE.md ~/.claude/CLAUDE.md

Customizing

Add personal preferences after the lab section:

## Personal Preferences

I prefer:
- Verbose explanations when learning new concepts
- Step-by-step breakdowns for complex tasks
- Asking before making changes to critical files

## My Projects

Active projects:
- ~/rashid-lab-setup/my-dissertation/ - Main research
- ~/rashid-lab-setup/side-project/ - Collaboration with X lab

~/.claude/settings.json

Global settings for permissions and plugins:

{
  "permissions": {
    "allow": [
      "Bash(Rscript *)",
      "Bash(git *)",
      "Bash(make *)",
      "Bash(quarto *)"
    ]
  }
}

Common Permission Patterns

{
  "permissions": {
    "allow": [
      "Bash(Rscript *)",
      "Bash(git *)",
      "Bash(make *)",
      "Bash(quarto *)",
      "Bash(sbatch *)",
      "Bash(squeue *)",
      "Bash(scancel *)",
      "Bash(srun *)",
      "Bash(module *)"
    ]
  }
}

PI Configuration

The PI template includes additional admin sections:

## Admin (PI Only)

### Student Management
See ~/rashid-lab-setup/lab-admin/ for:
- 1on1-meetings/ - Meeting notes
- milestones/ - PhD tracking
- config/students.yml - Student data

### Admin Commands
cd ~/rashid-lab-setup/lab-admin
make sync-students    # Propagate config
make prep-1on1        # Generate prep reports

### Team Account
Dashboard: https://claude.ai/team

Copy the PI template:

cp ~/rashid-lab-setup/lab-handbook/config/claude/pi-CLAUDE.md ~/.claude/CLAUDE.md

Project vs Global

Setting	Global (~/.claude/)	Project (.claude/)
Lab standards	✓
Personal preferences	✓
Project context		✓
Project skills		✓
Project agents		✓

Global settings provide defaults; project settings override them.

Syncing Across Machines

To use the same config on local and Longleaf:

# On Longleaf
mkdir -p ~/.claude

# Option 1: Copy from local
scp ~/.claude/CLAUDE.md <onyen>@longleaf.unc.edu:~/.claude/

# Option 2: Download from repo
curl -o ~/.claude/CLAUDE.md \
  https://raw.githubusercontent.com/rashidlab/lab-handbook/main/config/claude/student-CLAUDE.md

Troubleshooting

Global config not loading

# Check file exists
cat ~/.claude/CLAUDE.md

# Check permissions
ls -la ~/.claude/

Project overrides global

This is expected. Project .claude/CLAUDE.md takes precedence. To check which files Claude reads:

> What CLAUDE.md files are you reading?