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dnanexus-integration

Build and execute genomics workflows on DNAnexus using dxpy and dxapp.json.

22|4|Updated May 25, 2026
Search Tags:#bioinformatics#cloud#genomics#workflows#dxpy#dnanexus
One-click install
npx skills add https://github.com/crazymsn/academic-skills --skill dnanexus-integration-crazymsn
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: dnanexus-integration
Source: https://github.com/crazymsn/academic-skills/tree/main/academic-skills/dnanexus-integration
Command: npx skills add https://github.com/crazymsn/academic-skills --skill dnanexus-integration-crazymsn

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Solves the complexity of building, deploying, and orchestrating genomics workflows on DNAnexus by consolidating app development, data management, and job execution into a unified workflow.

Core Features & Use Cases

  • App Development: scaffold apps/applets with dx-app-wizard, generate dxapp.json, and structure src/ and resources/ for deployment.
  • Data Operations: manage uploads/downloads, search and organize data using dxpy, and automate project interactions.
  • Job Execution & Workflows: run applets/apps, monitor runtimes, and compose multi-step pipelines using DNAnexus workflows.
  • Python SDK dxpy: programmatic access to files, records, apps, and workflows, with linking and output references for automation.
  • Configuration & Dependencies: configure dxapp.json, specify execDepends, bundled resources, assets, and Docker-based environments.

Quick Start

Upload a sample input to DNAnexus, run a test applet, and retrieve the results.

Frequently Asked Questions about dnanexus-integration

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

FAQPage Schema
How do I build and deploy genomics apps on DNAnexus?▼

DNAnexus app deployment uses dx-app-wizard to scaffold projects, generate dxapp.json metadata, and structure src/ and resources/ directories for applet creation and execution.

Can I automate data uploads and project searches using dxpy?▼

Yes, the dxpy Python SDK enables programmatic access to manage uploads and downloads, search and organize data, and automate project interactions across DNAnexus platforms.

How do I configure Docker dependencies for a DNAnexus workflow?▼

Docker dependencies for DNAnexus workflows are configured within dxapp.json by specifying execDepends, bundled resources, assets, and Docker-based execution environments.

What is the best way to compose multi-step genomics pipelines in DNAnexus?▼

Multi-step genomics pipelines in DNAnexus are composed by running applets, monitoring runtimes, and linking output references between steps using DNAnexus workflow features.

Does DNAnexus integration support Python SDK access for workflow automation?▼

Yes, the integration provides programmatic access to files, records, apps, and workflows through the Python SDK dxpy, enabling linking and output references for automation.

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