Agent skill

Pharmgx Reporter

Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 31 SNPs, 51 drugs

Install Pharmgx Reporter

skills CLI

$ npx skills add ClawBio/ClawBio --skill pharmgx-reporter -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio pharmgx-reporter --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/pharmgx-reporter .claude/skills/pharmgx-reporter && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "pharmgx-reporter" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/pharmgx-reporter into .claude/skills/pharmgx-reporter/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pharmgx-reporter", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/ClawBio/ClawBio/tree/main/skills/pharmgx-reporter

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add ClawBio/ClawBio --skill pharmgx-reporter -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio pharmgx-reporter --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/pharmgx-reporter .agents/skills/pharmgx-reporter && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "pharmgx-reporter" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/pharmgx-reporter into .agents/skills/pharmgx-reporter/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pharmgx-reporter", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add ClawBio/ClawBio --skill pharmgx-reporter -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio pharmgx-reporter --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/pharmgx-reporter .cursor/skills/pharmgx-reporter && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "pharmgx-reporter" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/pharmgx-reporter into .cursor/skills/pharmgx-reporter/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pharmgx-reporter", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/ClawBio/ClawBio.git --path skills/pharmgx-reporter

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add ClawBio/ClawBio --skill pharmgx-reporter -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio pharmgx-reporter --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/pharmgx-reporter .gemini/skills/pharmgx-reporter && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "pharmgx-reporter" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/pharmgx-reporter into .gemini/skills/pharmgx-reporter/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pharmgx-reporter", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install ClawBio/ClawBio pharmgx-reporter

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add ClawBio/ClawBio --skill pharmgx-reporter -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/pharmgx-reporter .github/skills/pharmgx-reporter && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "pharmgx-reporter" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/pharmgx-reporter into .github/skills/pharmgx-reporter/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pharmgx-reporter", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add ClawBio/ClawBio --skill pharmgx-reporter -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio pharmgx-reporter --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/pharmgx-reporter .opencode/skills/pharmgx-reporter && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "pharmgx-reporter" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/pharmgx-reporter into .opencode/skills/pharmgx-reporter/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pharmgx-reporter", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: pharmgx-reporter
GitHub stars: 1.2k
Used in: 2 other repos
Token cost: ~1.5k tokens
SKILL.md length: 556 words
Files: 43
Skills in repo: 104
Repo updated: Oct 9, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 31 SNPs, 51 drugs

Works in 4 steps: Genotype Parsing: Auto-detects 23andMe… → Star Allele Calling: Maps diplotypes to… → Drug Recommendation: Looks up CPIC-level… → …
Research & Science work in your project
SKILL.md covers Why This Exists, Core Capabilities, Input Formats and Workflow, plus 9 more sections
Runs Python scripts from its folder; calls python

What it does

Pharmgx Reporter is an agent skill from ClawBio/ClawBio. Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 31 SNPs, 51 drugs

Its SKILL.md is about 1.5k tokens, which your agent loads only when the skill is triggered. The skill folder holds 49 other files (for example `INTENTS.json`, `api.py` and `demo_report/report.md`).

It sits in Research & Science. The repository describes itself as: 🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free. The licence is MIT.

When your agent uses it

Research & Science work in your project

Example prompts

“/pharmgx-reporter”

Requirements

Python 3

Workflow steps

4 steps, taken from the first numbered list in SKILL.md.

Genotype Parsing: Auto-detects 23andMe or AncestryDNA format, extracts 31 pharmacogenomic SNPs
Star Allele Calling: Maps diplotypes to metaboliser phenotypes (Poor, Intermediate, Normal, Rapid, Ultra-rapid)
Drug Recommendation: Looks up CPIC-level drug guidance for 51 medications across 12 genes
Single-Drug Mode: --drug flag for quick lookup of one medication (used by Drug Photo skill)

What it can do on your machine

Read from SKILL.md and the folder at commit dece754. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships script files (Python, from the files we listed), which the agent can run.
Shell commands in SKILL.md call:
- python
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
- cpicpgx.org
- fda.gov
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Pharmgx Reporter loads about 1.5k tokens when it runs. Until then it costs about 28 tokens; SKILL.md has 556 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~28
When it runs · the whole SKILL.md, loaded when a task matches: ~1.5k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from ClawBio/ClawBio at commit dece754, republished under its MIT licence (© ClawBio). 556 words, ~1,513 tokens.

Download SKILL.mdSave it as .claude/skills/pharmgx-reporter/SKILL.md (or your agent's skills folder). This skill also uses 42 other files; get the full folder from GitHub.

name: pharmgx-reporter
description: Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 31 SNPs, 51 drugs
license: MIT
metadata.version: 0.1.0
metadata.author: Manuel Corpas
metadata.tags: pharmacogenomics, CPIC, DTC-genetics, precision-medicine

💊 PharmGx Reporter

You are PharmGx Reporter, a specialised ClawBio agent for pharmacogenomic analysis. Your role is to generate a personalised drug–gene interaction report from consumer genetic data.

Why This Exists

Without it: Users must manually cross-reference their raw genotype files against CPIC guidelines — a multi-hour process requiring genetics expertise
With it: Upload a 23andMe or AncestryDNA file and get a structured report covering 12 genes and 51 drugs in seconds
Why ClawBio: Grounded in CPIC guidelines and FDA-approved PGx biomarkers, not LLM guesswork. Every recommendation traces to a published star-allele → phenotype → drug mapping.

Core Capabilities

Genotype Parsing: Auto-detects 23andMe or AncestryDNA format, extracts 31 pharmacogenomic SNPs
Star Allele Calling: Maps diplotypes to metaboliser phenotypes (Poor, Intermediate, Normal, Rapid, Ultra-rapid)
Drug Recommendation: Looks up CPIC-level drug guidance for 51 medications across 12 genes
Single-Drug Mode: --drug flag for quick lookup of one medication (used by Drug Photo skill)

Input Formats

Format	Extension	Required Fields	Example
23andMe raw data	`.txt`, `.txt.gz`	rsid, chromosome, position, genotype	`demo_patient.txt`
AncestryDNA raw data	`.txt`	rsid, chromosome, position, allele1, allele2	—

Reference genome build

Both GRCh37 and GRCh38 inputs are supported. Diplotypes are called by matching rsIDs, never by coordinate, so the same sample calls identically on either build. The reporter identifies the build from a five-SNP coordinate panel (chromosome and position must both agree) and states it in the report:

Detected	Behaviour
`GRCh38`	Called normally
`GRCh37`	Called normally; a note records that positions are GRCh37
`unknown_build`	All genes withheld as Indeterminate. Coordinates match neither build, so the file is corrupt, remapped or annotated against an unsupported assembly, and its rsIDs cannot be trusted either
(none)	No panel SNP carried a usable position; the build is not asserted

demo_patient.txt is genuine GRCh37 23andMe data and stays on GRCh37 deliberately, so the shipped demo exercises the GRCh37 path.

Show full SKILL.md (253 more words)Show less

Workflow

Parse: Read raw genetic data, auto-detect format (23andMe vs AncestryDNA)
Extract: Pull 31 PGx SNPs across 12 genes from the genotype file
Call: Determine star alleles and metaboliser phenotypes per gene
Lookup: Match each gene's phenotype to CPIC drug recommendations (AVOID / CAUTION / STANDARD / INSUFFICIENT)
Report: Generate report.md with gene profile table, drug summary, and clinical alerts

CLI Reference

bash

# Full report from patient data
python skills/pharmgx-reporter/pharmgx_reporter.py \
  --input <patient_file> --output <report_dir>

# Demo mode (synthetic 31-SNP patient)
python skills/pharmgx-reporter/pharmgx_reporter.py \
  --input skills/pharmgx-reporter/demo_patient.txt --output /tmp/pharmgx_demo

# Single-drug lookup (used by Drug Photo skill)
python skills/pharmgx-reporter/pharmgx_reporter.py \
  --input <patient_file> --drug Plavix

# Via ClawBio runner
python clawbio.py run pharmgx --demo
python clawbio.py run pharmgx --input <file> --output <dir>

Demo

bash

python clawbio.py run pharmgx --demo

Expected output: A multi-section report covering 12 gene profiles with metaboliser phenotypes, a 51-drug recommendation table (bucketed into AVOID / CAUTION / STANDARD / INSUFFICIENT), and a warfarin special alert (multi-gene CYP2C9 + VKORC1 interaction).

Genes Covered

CYP2C19, CYP2D6, CYP2C9, VKORC1, SLCO1B1, DPYD, TPMT, UGT1A1, CYP3A5, CYP2B6, NUDT15, CYP1A2

Drug Classes

Antiplatelet, opioids, statins, anticoagulants, PPIs, antidepressants (TCAs, SSRIs, SNRIs), antipsychotics, NSAIDs, oncology, immunosuppressants, antivirals

Output Structure

output_directory/
├── report.md              # Full pharmacogenomic report
├── result.json            # Machine-readable gene profiles + drug recommendations
└── reproducibility/
    └── commands.sh        # Exact command to reproduce

Dependencies

Required:

Python 3.10+ (standard library only — no external packages)

Safety

Local-first: Genetic data never leaves the machine
Disclaimer: Every report includes the ClawBio medical disclaimer
CPIC-grounded: All gene–drug mappings trace to published CPIC guidelines
No hallucinated associations: Only the 31 validated SNPs are used

Integration with Bio Orchestrator

Trigger conditions — the orchestrator routes here when:

User mentions pharmacogenomics, drug interactions, medications, CYP genes, warfarin, CPIC
User provides a 23andMe or AncestryDNA file and asks about drugs

Chaining partners:

drug-photo: Single-drug mode powers the photo → dosage card pipeline
profile-report: PharmGx results feed into the unified genomic profile
clinpgx: ClinPGx provides deeper gene-drug lookup when the user wants more detail

Citations

CPIC Guidelines — Clinical Pharmacogenetics Implementation Consortium
FDA Table of Pharmacogenomic Biomarkers — FDA-approved PGx drug labels

Files

SKILL.md and 42 other files in skills/pharmgx-reporter of ClawBio/ClawBio.

SKILL.md
INTENTS.json
api.py
demo_patient.txt
demo_report/report.md
evals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-0/criteria.json
evals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-0/inputs/patient_data.txt
evals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-0/scenario.json
evals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-0/task.md
evals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-2/criteria.json
evals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-2/inputs/ancestry_patient.txt
evals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-2/scenario.json
evals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-2/task.md
evals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-3
… and 29 more

Open the folder on GitHubat commit dece754

Used in 2 other repositories

We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 2 other GitHub owners. This page covers the copy in ClawBio/ClawBio, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Pharmgx Reporter next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Pharmgx Reporter compared with similar skills
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Pharmgx Reporter this skillClawBio/ClawBio	1.2k	2 repos	~1.5k	Automated safety check: Pass	MIT	2 days ago
Hypothesis Generationspacering-net/codeg	3.9k	14 repos	~3.6k	Automated safety check: Notes	MIT	today
GitHub Deep Researchbytedance/deer-flow	84k	4 repos	~1.3k	Automated safety check: Pass	MIT	today
Nature Paper CardYuan1z0825/nature-skills	47k	2 repos	~2.1k	Automated safety check: Pass	Apache-2.0	today
Content Research Writerweapp-tailwindcss/weapp-tailwindcss	1.9k	25 repos	~3.5k	Automated safety check: Pass	MIT	today
Last30daysmvanhorn/last30days-skill	64k	—	~7.9k	Automated safety check: Notes	MIT	yesterday

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Questions about Pharmgx Reporter

What does Pharmgx Reporter do?

Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 31 SNPs, 51 drugs. Pharmgx Reporter is an agent skill from ClawBio/ClawBio.

When should I use Pharmgx Reporter?

Pharmgx Reporter fits situations like: research & Science work in your project.

How do I install Pharmgx Reporter in Claude Code?

Run `npx skills add ClawBio/ClawBio --skill pharmgx-reporter -a claude-code`. Or copy the skill folder (skills/pharmgx-reporter in ClawBio/ClawBio) into .claude/skills/pharmgx-reporter in your project. Claude Code loads it when a task matches its description.

How do I install Pharmgx Reporter in Codex?

Run `npx skills add ClawBio/ClawBio --skill pharmgx-reporter -a codex`. Or copy the skill folder (skills/pharmgx-reporter in ClawBio/ClawBio) into .agents/skills/pharmgx-reporter in your project. Codex loads it when a task matches its description.

Can I use Pharmgx Reporter in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add ClawBio/ClawBio --skill pharmgx-reporter -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/pharmgx-reporter, .gemini/skills/pharmgx-reporter, .github/skills/pharmgx-reporter and .opencode/skills/pharmgx-reporter in your project.

What does Pharmgx Reporter need to run?

Going by SKILL.md and its folder, Pharmgx Reporter needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Pharmgx Reporter access the network?

SKILL.md names 2 domains. As links in the text: cpicpgx.org and fda.gov. This is read from the text; nothing was executed.

Is Pharmgx Reporter safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Pharmgx Reporter use?

Pharmgx Reporter is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Pharmgx Reporter use?

About 1.5k tokens (SKILL.md is roughly 6.1k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Pharmgx Reporter?

Skills that share tags, products or a category with Pharmgx Reporter: Hypothesis Generation (spacering-net/codeg, 3.9k stars), GitHub Deep Research (bytedance/deer-flow, 84k stars), Nature Paper Card (Yuan1z0825/nature-skills, 47k stars) and Content Research Writer (weapp-tailwindcss/weapp-tailwindcss, 1.9k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Pharmgx Reporter?

ClawBio (a GitHub organization) maintains it in ClawBio/ClawBio, which has 1,155 GitHub stars. The repository holds 104 skills in this directory. The repository was last updated on October 9, 2026.

Source: ClawBio/ClawBio on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Pharmgx Reporter

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

💊 PharmGx Reporter

Why This Exists

Core Capabilities

Input Formats

Reference genome build

Workflow

CLI Reference

Demo

Genes Covered

Drug Classes

Output Structure

Dependencies

Safety

Integration with Bio Orchestrator

Citations

Files

Used in 2 other repositories

Compare with similar skills

Similar skills

More from ClawBio/ClawBio

Related

Questions about Pharmgx Reporter