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fix(nutrigx-advisor): rename directory to conform to AgentSkills naming spec
The AgentSkills spec requires skill names to contain only lowercase letters, digits, and hyphens. Rename skills/nutrigx_advisor → skills/nutrigx-advisor and update all CLAUDE.md path references accordingly. Script filenames (nutrigx_advisor.py) are unchanged. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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‎CLAUDE.md‎

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@@ -10,7 +10,7 @@ When the user asks a question, match it to a skill and act:
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|---|---|---|
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| Drug interactions, pharmacogenomics, "what drugs should I worry about", 23andMe medications, CYP2D6, CYP2C19, warfarin, CPIC | `skills/pharmgx-reporter/` | Run `pharmgx_reporter.py` |
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| Genomic diversity, HEIM score, equity, population representation, FST, heterozygosity | `skills/equity-scorer/` | Run `equity_scorer.py` |
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| Nutrition, nutrigenomics, "what should I eat", diet genetics, MTHFR, folate, vitamin D, caffeine, lactose, omega-3 | `skills/nutrigx_advisor/` | Run `nutrigx_advisor.py` |
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| Nutrition, nutrigenomics, "what should I eat", diet genetics, MTHFR, folate, vitamin D, caffeine, lactose, omega-3 | `skills/nutrigx-advisor/` | Run `nutrigx_advisor.py` |
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| Ancestry, PCA, population structure, admixture, SGDP | `skills/claw-ancestry-pca/` | Read SKILL.md, apply methodology |
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| Semantic similarity, disease neglect, research gaps, NTDs, SII | `skills/claw-semantic-sim/` | Read SKILL.md, apply methodology |
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| Genome comparison, IBS, "how much DNA in common", George Church, Corpasome, pairwise | `skills/genome-compare/` | Run `genome_compare.py` |
@@ -51,7 +51,7 @@ When the user asks a question, match it to a skill and act:
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1. Read the skill's `SKILL.md` for domain context
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2. Run the Python script with correct CLI arguments (see below)
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3. Show the user the output — open any generated figures and explain results
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4. **DEMO FALLBACK (MANDATORY):** If the user has no input file, do NOT refuse or just ask for a file. Instead, immediately offer to run the skill with built-in demo/synthetic data (use the `--demo` flag or the demo files listed in the Demo Data table below). Say something like "I'll run a demo with synthetic data so you can see the report — here it is!" and then run it. Most skills support `--demo`. For pharmgx, use `--input skills/pharmgx-reporter/demo_patient.txt`. For nutrigx, use `--input skills/nutrigx_advisor/synthetic_patient.txt`. Every skill has demo data — never tell the user you can't run a skill because they don't have a file.
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4. **DEMO FALLBACK (MANDATORY):** If the user has no input file, do NOT refuse or just ask for a file. Instead, immediately offer to run the skill with built-in demo/synthetic data (use the `--demo` flag or the demo files listed in the Demo Data table below). Say something like "I'll run a demo with synthetic data so you can see the report — here it is!" and then run it. Most skills support `--demo`. For pharmgx, use `--input skills/pharmgx-reporter/demo_patient.txt`. For nutrigx, use `--input skills/nutrigx-advisor/synthetic_patient.txt`. Every skill has demo data — never tell the user you can't run a skill because they don't have a file.
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### Skills with SKILL.md only (no Python yet)
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1. Read the skill's `SKILL.md` thoroughly
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--input <vcf_or_csv> [--pop-map <csv>] [--output <dir>] [--weights 0.35,0.25,0.20,0.20]
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# Nutrigenomics advisor from genetic data
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python skills/nutrigx_advisor/nutrigx_advisor.py \
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python skills/nutrigx-advisor/nutrigx_advisor.py \
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--input <patient_file> --output <report_dir>
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# scRNA-seq pipeline from AnnData (.h5ad)
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| File | Location | Use With |
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|---|---|---|
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| Synthetic patient (PGx, 31 SNPs) | `skills/pharmgx-reporter/demo_patient.txt` | pharmgx-reporter |
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| Synthetic patient (NutriGx, 40 SNPs) | `skills/nutrigx_advisor/synthetic_patient.txt` | nutrigx_advisor |
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| Synthetic patient (NutriGx, 40 SNPs) | `skills/nutrigx-advisor/synthetic_patient.txt` | nutrigx_advisor |
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| PBMC3k raw demo (fallback synthetic) | `--demo` flag | scrna-orchestrator |
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| Demo VCF (50 samples, 5 populations) | `examples/demo_populations.vcf` | equity-scorer |
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| Population map | `examples/demo_population_map.csv` | equity-scorer |
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--input examples/sample_ancestry.csv --output /tmp/equity_csv_demo
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# NutriGx demo
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python skills/nutrigx_advisor/nutrigx_advisor.py \
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--input skills/nutrigx_advisor/synthetic_patient.txt --output /tmp/nutrigx_demo
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python skills/nutrigx-advisor/nutrigx_advisor.py \
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--input skills/nutrigx-advisor/synthetic_patient.txt --output /tmp/nutrigx_demo
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# MultiQC demo
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python skills/multiqc-reporter/multiqc_reporter.py --demo --output /tmp/multiqc_demo

skills/nutrigx_advisor/.gitignore renamed to skills/nutrigx-advisor/.gitignore

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skills/nutrigx_advisor/SKILL.md renamed to skills/nutrigx-advisor/SKILL.md

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---
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name: nutrigx-advisor
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description: Personalised nutrition report from consumer genetic data (23andMe, AncestryDNA, VCF) — interrogates nutritionally-relevant SNPs and generates actionable dietary guidance, all computed locally.
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version: 0.1.0
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author: David de Lorenzo
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description: Personalised nutrition report from consumer genetic data (23andMe, AncestryDNA, VCF) — interrogates nutritionally-relevant
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SNPs and generates actionable dietary guidance, all computed locally.
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license: MIT
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tags: [nutrigenomics, nutrition, diet, genetics, 23andme, ancestrydna, vcf]
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metadata:
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version: 0.1.0
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author: David de Lorenzo
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tags:
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- nutrigenomics
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- nutrition
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- diet
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- genetics
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- 23andme
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- ancestrydna
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- vcf
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openclaw:
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requires:
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bins:
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- python3
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env: []
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config: []
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- python3
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always: false
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emoji: "🥦"
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emoji: 🥦
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homepage: https://github.com/ClawBio/ClawBio
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os: [darwin, linux]
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os:
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- darwin
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- linux
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install:
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- kind: pip
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package: pandas numpy matplotlib seaborn
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bins: []
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- kind: pip
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package: reportlab
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bins: []
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- kind: pip
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package: pandas numpy matplotlib seaborn
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- kind: pip
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package: reportlab
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trigger_keywords:
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- personalised nutrition
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- nutrigenomics
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- diet genetics
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- MTHFR
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- APOE
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- FTO
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- vitamin D
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- caffeine metabolism
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- lactose
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- omega-3
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- folate
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- what should I eat based on my DNA
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- vitamin absorption genetics
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- gluten
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- personalised nutrition
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- nutrigenomics
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- diet genetics
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- MTHFR
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- APOE
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- FTO
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- vitamin D
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- caffeine metabolism
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- lactose
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- omega-3
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- folate
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- what should I eat based on my DNA
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- vitamin absorption genetics
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- gluten
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---
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# NutriGx Advisor — Personalised Nutrition from Genetic Data

skills/nutrigx_advisor/api.py renamed to skills/nutrigx-advisor/api.py

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skills/nutrigx_advisor/data/snp_panel.json renamed to skills/nutrigx-advisor/data/snp_panel.json

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skills/nutrigx_advisor/examples/data/.gitkeep renamed to skills/nutrigx-advisor/examples/data/.gitkeep

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skills/nutrigx_advisor/examples/generate_patient.py renamed to skills/nutrigx-advisor/examples/generate_patient.py

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skills/nutrigx_advisor/examples/output/nutrigx_heatmap.png renamed to skills/nutrigx-advisor/examples/output/nutrigx_heatmap.png

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skills/nutrigx_advisor/examples/output/nutrigx_radar.png renamed to skills/nutrigx-advisor/examples/output/nutrigx_radar.png

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skills/nutrigx_advisor/examples/output/nutrigx_report.md renamed to skills/nutrigx-advisor/examples/output/nutrigx_report.md

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