Centralized Claude Code Skills & Commands

Reusable Claude Code skills and commands for all projects via symlinks.

📋 Quick Start: See QUICK_REFERENCE.md for copy-paste setup prompts and commands.

Directory Structure

$CLAUDE_METADATA/
├── skills/                    # All reusable skills (organized by category)
│   ├── claude-meta/          # Claude Code usage & optimization
│   ├── project-management/   # Project setup & organization
│   ├── packaging/            # Package development
│   ├── galaxy/               # Galaxy platform
│   ├── bioinformatics/       # Domain-specific bio skills
│   ├── analysis/             # Data analysis & notebooks
│   ├── collaboration/        # Sharing & collaboration
│   └── INDEX.md              # Comprehensive skills catalog
├── commands/                  # Slash commands
│   ├── global/               # All projects
│   └── vgp-pipeline/         # Project-specific
└── templates/                # Templates for new skills/commands

How It Works

Claude Code discovers skills from:

• ~/.claude/skills/ (global)
• .claude/skills/ (per-project)

Skills load progressively - Claude sees descriptions first, full content only when activated.

Available Skills

📚 See skills/INDEX.md for the complete catalog with detailed descriptions, use cases, and dependencies.

Essential Skills (Always Include)

• claude-meta/token-efficiency - Automatic token optimization (80-90% savings)
• claude-meta/collaboration - Team collaboration best practices
• project-management/managing-environments - Development environment management (venv/conda)
• project-management/folder-organization - Project structure and organization

Skills by Category

• Claude Meta (3 skills) - Claude Code usage, collaboration, optimization
• Project Management (2 skills) - Project setup, folder organization, environment management
• Packaging (1 skill) - Bioconda recipe development
• Galaxy (3 skills) - Galaxy platform development & automation
• Bioinformatics (2 skills) - Genome assembly, sequencing analysis
• Analysis (1 skill) - Jupyter notebooks, statistical analysis
• Collaboration (2 skills) - Project sharing, collaborative documentation

Browse the full catalog: skills/INDEX.md

Global Commands (commands/global/)

• /setup-project - Initialize new project with essential skills
• /setup-environment - Plan and set up Python environment (venv or conda)
• /sync-skills - Sync with $CLAUDE_METADATA, detect new skills
• /list-skills - Show all available skills
• /update-skills - Review session and update skills
• /cleanup-project - Remove working docs, condense verbose READMEs

Setting Up a New Project

Quick Start:

/setup-project  # Auto-detects project type and sets up skills

Manual Setup:

mkdir -p .claude/skills .claude/commands

# Essential skills (always include)
ln -s $CLAUDE_METADATA/skills/claude-meta/token-efficiency .claude/skills/
ln -s $CLAUDE_METADATA/skills/claude-meta/collaboration .claude/skills/
ln -s $CLAUDE_METADATA/skills/project-management/managing-environments .claude/skills/
ln -s $CLAUDE_METADATA/skills/project-management/folder-organization .claude/skills/

# Global commands (always include)
ln -s $CLAUDE_METADATA/commands/global/*.md .claude/commands/

# Project-specific skills (add as needed)
ln -s $CLAUDE_METADATA/skills/galaxy/automation .claude/skills/  # For Galaxy projects
ln -s $CLAUDE_METADATA/skills/bioinformatics/vgp-pipeline .claude/skills/  # For VGP projects
ln -s $CLAUDE_METADATA/skills/category/your-skill .claude/skills/

See QUICK_REFERENCE.md for detailed prompts and workflows.

Adding New Skills/Commands

Using templates (recommended):

./templates/create-skill.sh my-skill "Description"
./templates/create-command.sh category cmd-name "Description"

Manual:

# Skill (choose appropriate category: claude-meta, environments, galaxy, bioinformatics, analysis, tools)
mkdir skills/category/my-skill
cat > skills/category/my-skill/SKILL.md << 'EOF'
---
name: my-skill
description: Brief description
version: 1.0.0
---
# Skill content...
EOF

# Update skills/INDEX.md with the new skill

# Command
cat > commands/global/my-cmd.md << 'EOF'
---
name: my-cmd
description: Brief description
---
Command prompt...
EOF

See templates/README.md for details.

Troubleshooting

Skill not activating:

• Mention skill name explicitly
• Check ls -la .claude/skills/ for symlink
• Verify SKILL.md has frontmatter

Command not found:

• Check ls -la .claude/commands/
• Verify command has frontmatter
• Restart Claude Code session

Symlink issues:

• Use absolute paths: $CLAUDE_METADATA/...
• Check target exists and permissions