Claude Code Global Skills Repository
Centralized skills and commands for Claude Code, symlinked into projects via enable-skills.sh. All projects share and auto-update from this single source.
Table of Contents
Setup
# Set environment variable (add to ~/.zshrc)
export CLAUDE_METADATA="$HOME/Workdir/claude_global"
# Enable skills in a project
cd /path/to/your/project
bash $CLAUDE_METADATA/enable-skills.sh
The setup script detects project type and suggests appropriate skills:
| Project Type |
Suggested Skills |
| Analysis/Research |
All analysis/*, bioinformatics/*, databases/*, collaboration/hackmd, collaboration/project-sharing |
| Development |
packaging/conda-recipe |
| Bioinformatics |
All galaxy/* |
All claude-meta/* and project-management/* skills are always included as essentials.
Skills
Analysis
| Skill |
Description |
data-analysis-patterns |
Data aggregation, recalculation vs reuse, category management, analytical accuracy. |
data-visualization |
Publication-quality figures with matplotlib/seaborn. Journal-specific .mplstyle files (Nature/Science/Cell), colorblind-safe palettes, figure export helpers, Claude API image constraints. |
documentation-organization |
Structure working files, prepare sharing packages, clean project layout. |
jupyter-notebook |
Comprehensive notebook analyses with statistical rigor, outlier handling, publication-quality visualizations. |
scientific-publication |
Iterative refinement of publication figures — systematic improvement, layout optimization. |
| Skill |
Description |
fundamentals |
SAM/BAM, AGP, sequencing technologies (Hi-C, HiFi, Illumina), quality metrics, alignment debugging. |
phylogenetics |
Phylogenetic tree analysis, visualization, annotation management, iTOL troubleshooting. |
visualization |
Publication-quality bioinformatics figures — phylogenetic trees, genome browsers, iTOL datasets. |
Essential skills defining how Claude works with you. Auto-included in all projects.
| Skill |
Description |
collaboration |
Team workflows — skill management, knowledge capture, version control. |
documentation |
Session documentation — incremental summaries, fix reports, audit trails. |
skill-management |
Creating, symlinking, updating, and organizing the centralized skill repository. |
systematic-debugging |
4-phase debugging: root cause → pattern analysis → hypothesis → fix. Anti-rationalization tables. |
token-efficiency |
Token optimization — efficient file reading, command execution, model selection (Opus for learning, Sonnet for dev). |
verification-before-completion |
Evidence-based completion claims. Run verification before claiming success. |
Collaboration
| Skill |
Description |
hackmd |
Slide presentations, embedded SVG diagrams, real-time collaborative editing. |
project-sharing |
Prepare organized sharing packages at different levels (Summary/Reproducible/Full). |
Databases
| Skill |
Description |
bioservices |
Unified Python interface to 40+ bioinformatics services (UniProt, KEGG, ChEMBL, Reactome, PSICQUIC). Cross-database analysis and ID mapping. |
gget |
Fast CLI/Python queries to 20+ databases — gene info, BLAST, AlphaFold, enrichment, single-cell, disease associations. |
gnomad |
gnomAD GraphQL API — population allele frequencies, constraint scores (pLI, LOEUF), variant pathogenicity, ACMG criteria. |
Galaxy
| Skill |
Description |
automation |
BioBlend and Planemo — Galaxy API, workflow invocation, batch processing, dataset management. |
tool-wrapping |
Galaxy tool wrapper XML, Planemo testing, best practices. |
training-material |
GTN tutorial development — markdown syntax, special boxes, tool references, YAML front matter. |
workflow-development |
Galaxy .ga workflows, IWC standards, testing, optimization. |
Packaging
| Skill |
Description |
conda-recipe |
Conda/bioconda recipe creation, linting, dependency management, build debugging. |
Project Management
Essential skills. Auto-included in all projects.
| Skill |
Description |
data-backup |
Smart backups with project type detection. Rolling daily, compressed milestones, CHANGELOG. |
folder-organization |
Project folder structure, file naming conventions, directory standards. |
managing-environments |
Python venv and conda environment management. |
obsidian |
Obsidian vault integration — notes, tasks, knowledge management, MOCs, CLI (1.12+). |
VGP
| Skill |
Description |
genomeark-aws |
GenomeArk AWS S3 bucket — VGP assemblies, QC data, species directories. |
vgp-pipeline |
VGP assembly pipeline — Galaxy workflow selection, QC checkpoints, batch orchestration. |
Commands
Session Management
| Command |
Description |
/safe-exit |
End session with backup and Obsidian summary. |
/safe-clear |
Save notes to Obsidian, update skills, clear context. |
Project Organization
| Command |
Description |
/backup |
Smart backup with skill-aware cleanup. |
/consolidate-notes |
Consolidate session notes with AI-powered analysis. |
/cleanup-project |
Remove working docs, condense verbose READMEs. |
/deprecate-file |
Move files to deprecated/ with dependency handling. |
/share-project |
Prepare sharing packages (Summary/Reproducible/Full). |
Navigation & Discovery
| Command |
Description |
/command-help |
Show help for any command. |
/list-skills |
List all available skills with descriptions. |
/read-manifest |
Smart session startup — load relevant context. |
/generate-manifest |
Generate or update MANIFEST.md file inventories. |
/update-manifest |
Quick-update MANIFEST.md preserving user content. |
Setup & Maintenance
| Command |
Description |
/setup-project |
Set up Claude Code skills for a new project. |
/setup-environment |
Plan and set up Python venv or conda environment. |
/sync-skills |
Sync project with global metadata — detect new skills/commands. |
/update-skills |
Review session and suggest skill updates. |
/update-notebook |
Notebook maintenance — figures, references, TOC, coherence. |
Planning
| Command |
Description |
/design-and-plan |
Brainstorm → design → plan → execute workflow for complex tasks. |
/plan-interview |
Deep interactive Q&A about a plan, then rewrites it with your answers. |
/plan-research-questions |
Parallel subagents research each open question in a plan. |
/plan-integrate-questions |
Merge answered questions back into the plan body. |
/plan-review |
Review an unimplemented plan for clarity, correctness, and feasibility. |
/plan-debrief |
Compare implementation against a plan — find gaps and propose next steps. |
/plan-summary |
Summarize next steps from a plan with repo verification. |
/plan-clean |
Renumber phases/steps sequentially and update all cross-references. |
Code Quality
| Command |
Description |
/dedup |
Semantic duplication analysis with concrete refactoring recommendations. |
/review-test |
Review tests for quality — challenge weak assertions, find dead tests. |
/challenge-mocks |
Challenge Python mock/patch usage, suggest DI, fakes, and real alternatives. |
Git Workflow
| Command |
Description |
/decompose-for-rebase |
Break a messy commit into smaller, focused commits for interactive rebase. |
/deconflict |
Resolve rebase/merge conflicts with clear explanation. |
Clipboard Utilities
| Command |
Description |
/clipdoc |
Copy file contents to the system clipboard. |
/clippath |
Copy a file's absolute path to the system clipboard. |
Attribution:
Hooks
Hooks live in hooks/ and are symlinked to ~/.claude/hooks/. Configured in ~/.claude/settings.json with portable ~/ paths.
# Setup on a new machine
mkdir -p ~/.claude/hooks
ln -s $CLAUDE_METADATA/hooks/safety ~/.claude/hooks/safety
ln -s $CLAUDE_METADATA/hooks/peon-ping ~/.claude/hooks/peon-ping
Safety Hooks (hooks/safety/)
| Hook |
Matcher |
What it does |
git-guard.sh |
Bash |
Blocks reset --hard, push --force, clean -f, checkout -- ., stash drop/clear, branch -D |
protect-files.sh |
Write|Edit |
Blocks edits to .env, raw/, datasets/, .log, lock files |
Context Preservation
| Hook |
Event |
What it does |
context-reinject.sh |
SessionStart / compact |
Re-injects branch, commits, conda env, project-config, and PROGRESS.md after compaction |
transcript-backup.sh |
PreCompact |
Saves transcript before compaction (keeps last 20) |
Progress Tracking
| Hook |
Event |
What it does |
| Prompt hook |
SessionEnd (clear|logout|prompt_input_exit) |
Claude writes/updates PROGRESS.md with task summary, accomplishments, next steps, key decisions. Also updates MANIFEST.md if present. |
| Prompt hook |
PreCompact |
Same as above — preserves context before compaction |
progress-update-fallback.sh |
SessionEnd, PreCompact |
Fallback if prompt hook fails — writes mechanical PROGRESS.md from git state (branch, recent commits, changed files) or filesystem (recent files, project contents). Skips if PROGRESS.md was updated in the last 60s. |
Auto-formatting (PostToolUse, async)
| Hook |
Matcher |
What it does |
auto-format.sh |
Edit|Write |
Runs ruff format on .py files |
notebook-strip.sh |
Edit|Write|NotebookEdit |
Runs nbstripout on .ipynb files |
command-audit.sh |
Bash |
Logs commands to .claude/command-audit.log |
Peon Ping (hooks/peon-ping/)
Sound notification system that plays audio cues on hook events (session start/end, tool use, errors, etc.). Supports multiple voice packs, volume control, and push notifications (ntfy, Pushover, Telegram) via environment variables.
| Config |
Description |
config.json |
Volume, active pack, rotation mode, notification settings |
packs/ |
Voice pack sound files |
scripts/ |
Helper scripts for renaming, usage tracking |
Adding New Skills
mkdir skills/category/my-skill
# Create SKILL.md with frontmatter (name, description, version, allowed-tools)
# Keep SKILL.md under 500 lines — move details to supporting files
# Add to enable-skills.sh suggested list if appropriate
See skills/claude-meta/skill-management/ for the complete guide.
