token-efficiency
delphine-l/claude_global · skills.sh
Open source Repository Open in the app JSON README (API)
About
Skill publicada por delphine-l/claude_global no skills.sh. Instale com: npx skills add delphine-l/claude_global@token-efficiency
Details
- Kind
- Agent skills
- Topic
- No topic detected
- Publisher
- delphine-l
- Origin
- skillssh
- Category
- ferramentas
- Stars
- 19
- Forks
- 2
- Last push
- 2026-05-14T20:56:04Z
- Repository state
- ativo
- Language
- Shell
- Added
- 2026-08-30 15:22:09
- Updated
- 2026-09-08 15:04:37
- Origin id
delphine-l/claude_global/token-efficiency
README
# 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](#setup) - [Skills](#skills) - [Analysis](#analysis) - [Bioinformatics](#bioinformatics) - [Claude Meta](#claude-meta) (essential — auto-included) - [Collaboration](#collaboration) - [Databases](#databases) - [Galaxy](#galaxy) - [Packaging](#packaging) - [Project Management](#project-management) (essential — auto-included) - [VGP](#vgp) - [Commands](#commands) - [Hooks](#hooks) - [Adding New Skills](#adding-new-skills) ## Setup ```bash # 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](https://github.com/obra/superpowers/) brainstorming and writing-plans skills. > - Planning suite, git workflow, code quality, and clipboard commands adapted from [jmchilton/claude-jmchilton-plugins](https://github.com/jmchilton/claude-jmchilton-plugins) and [jmchilton/claude-commands](https://github.com/jmchilton/claude-commands). ## Hooks Hooks live in `hooks/` and are symlinked to `~/.claude/hooks/`. Configured in `~/.claude/settings.json` with portable `~/` paths. ```bash # 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 ```bash 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.