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Pharmgx Reporter
by
manuelcorpas
· GitHub ↗
· v0.1.0
427
Downloads
0
Stars
0
Active Installs
1
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Install in OpenClaw
/install clawbio-pharmgx-reporter
Description
Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA)
README (SKILL.md)
PharmGx Reporter
Generate a pharmacogenomic report from consumer genetic data (23andMe, AncestryDNA).
What it does
- Parses raw genetic data files (auto-detects 23andMe or AncestryDNA format)
- Extracts 31 pharmacogenomic SNPs across 12 genes
- Calls star alleles and determines metabolizer phenotypes
- Looks up CPIC drug recommendations for 51 medications
- Generates a markdown report with gene profiles, drug tables, and alerts
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
Usage
python pharmgx_reporter.py --input patient_data.txt --output report
Disclaimer
This tool is for research and educational purposes only. It is NOT a diagnostic device. Always consult a healthcare professional before making any medication decisions.
Usage Guidance
This skill appears to be a coherent, local pharmacogenomics report generator. Before installing or running it: (1) remember genetic data is highly sensitive — run the script locally on a machine you control and avoid uploading raw data to unknown services; (2) review the full pharmgx_reporter.py yourself (or run it in a sandbox) to confirm it behaves as expected; (3) do not treat the output as clinical advice — the SKILL.md disclaimer is appropriate and you should consult a healthcare professional for any medication decisions; (4) note the package metadata/source is not authoritative in the registry listing — if provenance matters, verify the upstream repository referenced in SKILL.md (MIT license) and the author identity before use.
Capability Analysis
Type: OpenClaw Skill
Name: clawbio-pharmgx-reporter
Version: 0.1.0
The skill is classified as suspicious due to a lack of input sanitization in `pharmgx_reporter.py`. The script embeds the user-provided input filename directly into a shell command string within the generated `report.md` file (in the 'Reproducibility' section). If a malicious filename (e.g., `'; rm -rf /'`) is provided, and the generated command from the report is subsequently executed by a shell, it could lead to arbitrary command execution (shell injection). This is a vulnerability, not intentional malice, aligning with the 'suspicious' classification criteria.
Capability Assessment
Purpose & Capability
The name and description (generate a pharmacogenomic report from 23andMe/AncestryDNA data) match the included SKILL.md and the bundled Python script which implements SNP parsing, phenotype rules, and report generation. No unrelated cloud credentials or unrelated binaries are requested. Note: registry metadata at the top listed no homepage/source, while SKILL.md contains a GitHub homepage URL — a minor metadata mismatch but not a functional inconsistency.
Instruction Scope
SKILL.md instructs running the included Python script on a local input file and producing a markdown report. The instructions do not ask the agent to read other system files, environment variables, or to send data externally. The Python file (visible imports) uses only standard libraries (argparse, hashlib, os, re, sys, datetime, pathlib) consistent with local parsing and report writing.
Install Mechanism
There is no install spec (instruction-only skill) and no external downloads or package installs declared. The bundle includes the script itself, so nothing is fetched from third-party URLs during install.
Credentials
The skill declares no required environment variables, no credentials, and no config paths. This is proportional for a local file-parsing/reporting tool.
Persistence & Privilege
The skill does not request always:true and is user-invocable only; it does not ask to modify other skills or system-wide settings. Autonomous invocation is permitted by default but not combined with other red flags.
How to Use
- Make sure OpenClaw is installed (local or Docker)
- Run the install command in chat:
/install clawbio-pharmgx-reporter - After installation, invoke the skill by name or use
/clawbio-pharmgx-reporter - Provide required inputs per the skill's parameter spec and get structured output
Version History
v0.1.0
Initial release of PharmGx Reporter – generate a pharmacogenomic report from DTC genetic data.
- Parses 23andMe or AncestryDNA raw genetic files and auto-detects the format.
- Extracts 31 pharmacogenomic SNPs across 12 genes relevant to drug response.
- Calls star alleles and determines metabolizer phenotypes.
- Provides CPIC-based recommendations for 51 medications, covering multiple drug classes.
- Outputs a comprehensive markdown report with gene profiles, drug recommendations, and safety alerts.
Metadata
Frequently Asked Questions
What is Pharmgx Reporter?
Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA). It is an AI Agent Skill for Claude Code / OpenClaw, with 427 downloads so far.
How do I install Pharmgx Reporter?
Run "/install clawbio-pharmgx-reporter" in the OpenClaw or Claude Code chat to install it in one step — no extra setup required.
Is Pharmgx Reporter free?
Yes, Pharmgx Reporter is completely free (open-source). You can download, install and use it at no cost.
Which platforms does Pharmgx Reporter support?
Pharmgx Reporter is cross-platform and runs anywhere OpenClaw / Claude Code is available (cross-platform).
Who created Pharmgx Reporter?
It is built and maintained by manuelcorpas (@manuelcorpas); the current version is v0.1.0.
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