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dnanexus-integration

Automate DNAnexus data management and genomics workflow execution via dxpy SDK.

16|7|Updated Nov 20, 2025
Search Tags:#genomics#app-development#dxpy#data-operations#dnanexus
One-click install
npx skills add https://github.com/jackspace/ClaudeSkillz --skill dnanexus-integration
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: dnanexus-integration
Source: https://github.com/jackspace/ClaudeSkillz/tree/main/skills/scientific-integration-dnanexus-integration
Command: npx skills add https://github.com/jackspace/ClaudeSkillz --skill dnanexus-integration

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

DNAnexus automation enables scalable genomics data processing by uploading data, running apps, and retrieving outputs via the dxpy Python SDK.

Core Features & Use Cases

  • App development, data upload/download, and workflow execution
  • Batch processing patterns across multiple files
  • Python SDK-based automation for reproducible genomics pipelines

Quick Start

Upload a FASTQ file, run an applet, and download the aligned BAM.

Frequently Asked Questions about dnanexus-integration

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I automate genomics workflows with the DNAnexus SDK?▼

Automate genomics workflows using dxpy to upload FASTQ/BAM/VCF files, execute applets, and download results programmatically. The dxpy SDK enables multi-step pipeline orchestration and batch processing across DNAnexus without manual intervention.

Can I build and deploy custom apps on DNAnexus?▼

Yes. Build applets using dxapp.json metadata and Docker containers, then deploy via dxpy. Configure resource allocation, manage dependencies, and control job execution across distributed genomics analyses.

What file formats does DNAnexus app automation support?▼

DNAnexus automation supports FASTQ, BAM, and VCF file formats natively through dxpy data operations. Upload, organize, search, and process these genomics formats at scale within orchestrated pipelines.

How do I batch process multiple genomics files on DNAnexus?▼

Use dxpy scripting to iterate over files in DNAnexus storage, trigger applets for each input, and collect outputs. Batch patterns automate multi-file workflows like alignment or variant calling reproducibly.

Does DNAnexus work with Docker containers for custom analysis tools?▼

Yes. Package custom genomics tools in Docker containers and integrate them into DNAnexus applets via dxapp.json. This enables reproducible, scalable deployment of proprietary or specialized analysis code.

What's required to start automating data management on DNAnexus?▼

Python environment, dxpy SDK installation, and DNAnexus account credentials. Prerequisites include understanding applet structure, file organization, and basic dxpy API calls for upload, execution, and retrieval.

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