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
• Skills
  • Analysis
  • Bioinformatics
  • Claude Meta (essential — auto-included)
  • Collaboration
  • Databases
  • Galaxy
  • Packaging
  • Project Management (essential — auto-included)
  • VGP
• Commands
• Hooks
• Adding New Skills

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.

Bioinformatics

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.

Claude Meta

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:

• /design-and-plan inspired by obra/superpowers brainstorming and writing-plans skills.
• Planning suite, git workflow, code quality, and clipboard commands adapted from jmchilton/claude-jmchilton-plugins and jmchilton/claude-commands.

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/)

Blocking (PreToolUse)

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.