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my_claude_skills

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Claude Skill to prevent automatic confirmatory answers

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# B. de Medeiros' Claude Skills Collection

Custom Claude skills for enhanced reasoning, bioinformatics, accounting, and natural history museum workflows. Each skill is a self-contained module bundled into installable plugins.

## Available Plugins and Skills

### general-skills

| Skill | Description |
|-------|-------------|
| **extract-from-pdfs** | 8-step pipeline for extracting structured data from scientific PDFs using Claude's vision. Supports abstract filtering (Ollama/Haiku/Sonnet), external validation (GBIF, WFO, GeoNames, PubChem, NCBI), and export to multiple formats. [Docs →](./extract_from_pdfs/README.md) |
| **document-ocr** | Converts scanned PDFs and document images into clean Markdown using docling for layout (figures, tables, reading order) plus a vision-language OCR model. Preserves multi-column order, diacritics, and figures. Supports local vLLM/Ollama and cloud vision APIs (OpenAI, Anthropic). [Docs →](./document_ocr/SKILL.md) |
| **accounting** | Processes procurement card receipts, tracks expenses in Google Sheets, reconciles records, and generates entertainment supplement tables. Reads SmartData statement exports to record the posted USD amount on international charges, add the 1% cross-border fee as its own row, and flag posted charges that were never recorded. [Docs →](./accounting/SKILL.md) |
| **lab-ordering** | Places lab supply orders from member requests. Routes by request header to Amazon Business, the Pritzker Lab Google Form, or a direct vendor; stages the cart/form and stops for human review before any purchase. [Docs →](./lab_ordering/SKILL.md) |
| **secure-raw-data-backup** | Archives irreplaceable raw data to write-once cloud cold storage. Generates and verifies md5 checksums, streams an uncompressed tarball to S3 Deep Archive under Object Lock with no local temp copy, writes an instantly-readable manifest as the completion marker, and proves the pipeline with a restore test before trusting it at scale. [Docs →](./secure_raw_data_backup/SKILL.md) |

### bioinfo-skills

| Skill | Description |
|-------|-------------|
| **phylo-from-buscos** | Generates phylogenomic workflows from genome assemblies using BUSCO/compleasm single-copy orthologs. Supports NCBI accessions, multiple schedulers (SLURM, PBS, local), concatenated and coalescent phylogenies. [Docs →](./phylo_from_buscos/README.md) |
| **biogeobears** | Sets up BioGeoBEARS biogeographic analyses in R. Validates inputs, generates RMarkdown scripts, compares DEC/DIVALIKE/BAYAREALIKE models, and produces publication-ready ancestral range visualizations. [Docs →](./biogeobears/README.md) |

### museum-skills

| Skill | Description |
|-------|-------------|
| **emu-bulk-upload** | Helps FMNH entomology curators bulk upload specimen data to the Emu database. Matches localities to existing records, creates new site records, and generates formatted upload tables. [Docs →](./Emu_bulk_upload_FMNH/SKILL.md) |
| **nirc-badge-request** | Prepares FMNH NIRC ID badge requests (Scientific Affiliate, Visitor, Contractor) and prefills the NIRC Badge Request Google Form for review. Gates on curator status, validates lead time and after-hours rules, and never submits. [Docs →](./nirc_badge_request/SKILL.md) |

## Installation

### Claude Code — CLI, VS Code, or JetBrains (Recommended)

These instructions work the same way in:
- **Claude Code CLI** — type commands directly in the terminal
- **VS Code** — type commands in the Claude Code chat panel (or use `/plugins` to open the visual manager)
- **JetBrains IDEs** — type commands in the Claude Code panel

#### Step 1: Add the marketplace

You only need to do this once:

```
/plugin marketplace add brunoasm/my_claude_skills
```

#### Step 2: Install the plugins you need

Install all plugins:
```
/plugin install general-skills@brunoasm/my_claude_skills
/plugin install bioinfo-skills@brunoasm/my_claude_skills
/plugin install museum-skills@brunoasm/my_claude_skills
```

Or install only the ones you want — each plugin is independent.

#### Install from a local clone

```bash
git clone https://github.com/brunoasm/my_claude_skills.git
cd my_claude_skills
```
Then in Claude Code:
```
/plugin marketplace add .
/plugin install general-skills@.
```

#### Scope options

When installing, Claude Code will ask you to choose a scope:
- **User** — available in all your projects
- **Project** — shared with collaborators via `.claude/settings.json`
- **Local** — only you, only this repo

### Claude.ai (Web)

1. Download the zip file for the desired skill from [releases](https://github.com/brunoasm/my_claude_skills/releases)
2. Go to Claude.ai **Settings > Capabilities > Skills**
3. Click **Upload Skill** and select the ZIP file
4. Enable the skill

## Resources

- [Claude Code Plugins Documentation](https://code.claude.com/docs/en/plugins.md)
- [Claude Code Skills Documentation](https://code.claude.com/docs/en/skills.md)
- [Claude.ai](https://claude.ai)

my_claude_skills

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