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dnanexus-integration

Build DNAnexus apps, manage FASTQ/BAM/VCF data, and orchestrate dxpy jobs.

4|Updated Mar 2, 2026
Search Tags:#workflow orchestration#data management#dxpy#dnanexus#fastq#genomics pipelines#applet development
One-click install
npx skills add https://github.com/shushuzn/Rairos --skill dnanexus-integration-shushuzn
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: dnanexus-integration
Source: https://github.com/shushuzn/Rairos/tree/main/skills/dnanexus-integration
Command: npx skills add https://github.com/shushuzn/Rairos --skill dnanexus-integration-shushuzn

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

DNAnexus Integration helps you build and operate end-to-end genomics workflows by providing reliable patterns to develop DNAnexus apps/applets, manage sequencing data, and run analyses using dxpy or DNAnexus CLI.

Core Features & Use Cases

  • App/Applet development: Generate applets, implement Python/Bash entry points, define dxapp.json, and deploy executables for genomics tasks.
  • Data operations: Upload/download FASTQ/BAM/VCF and other objects, manage records/metadata, and search/organize data by properties and project context.
  • Job execution & workflows: Launch jobs and chained workflows, monitor status/logs, and orchestrate parallel scatter-gather pipelines.
  • dxpy Python SDK integration: Script automation for data movement, job launching, output reference chaining, and platform API access.
  • Configuration & dependencies: Package runtime dependencies via execDepends, bundled resources, assets, or Docker, with resource/timeout configuration.

Quick Start

Use the dnanexus-integration skill to upload a FASTQ file to a DNAnexus project and run a DNAnexus applet that outputs aligned BAM files, then download the result to your local machine.

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 a DNAnexus applet using dxpy?▼

To build a DNAnexus applet, define a dxapp.json configuration, implement Python or Bash entry points, package dependencies via execDepends or Docker, and deploy the executable using dxpy APIs.

How do I upload FASTQ files and run a pipeline on DNAnexus?▼

Upload FASTQ files to a DNAnexus project using dxpy, launch an applet to process sequencing data into aligned BAM files, monitor job status, and download the output objects to your local machine.

What is the best way to orchestrate parallel scatter-gather genomics pipelines in DNAnexus?▼

Orchestrate scatter-gather genomics pipelines by chaining multi-step workflows with parallel subjobs, using dxpy to launch jobs, monitor execution logs, and retrieve output references for downstream analysis.

Can I manage FASTQ, BAM, and VCF data objects within a DNAnexus project?▼

You can manage FASTQ, BAM, and VCF data objects by using dxpy to upload, download, and search project data, organizing records by metadata properties while handling correct object lifecycle states.

Do I need a DNAnexus account to run genomics workflows with dxpy?▼

Yes, you need a DNAnexus account with authentication configured via the dxpy Python SDK or the DNAnexus CLI to access project data, launch jobs, and manage genomics pipelines.

How do I package runtime dependencies for a DNAnexus applet?▼

Package runtime dependencies for a DNAnexus applet by defining execDepends in dxapp.json, bundling resources, using assets, or configuring a Docker image with appropriate resource and timeout settings.

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