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dnanexus-integration

Automate DNAnexus app creation, data operations, and workflow execution with dxpy scripting.

74|5|Updated Dec 10, 2025
Search Tags:#workflow#bioinformatics#genomics#pipeline#dxpy#dnanexus#applet
One-click install
npx skills add https://github.com/dralkh/seerai --skill dnanexus-integration-dralkh
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: dnanexus-integration
Source: https://github.com/dralkh/seerai/tree/main/skills/dnanexus-integration
Command: npx skills add https://github.com/dralkh/seerai --skill dnanexus-integration-dralkh

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill removes the complexity of building, configuring, and operating DNAnexus-based genomics workflows so you can focus on analysis instead of platform mechanics.

Core Features & Use Cases

  • App and applet development for Python or Bash executables on DNAnexus.
  • Data operations for uploading, downloading, searching, cloning, and organizing files and records.
  • Job execution and workflow orchestration, including monitoring, chaining outputs, and parallel subjobs.
  • dxpy Python SDK guidance for scripting platform automation and API access.
  • Configuration help for dxapp.json, dependencies, instance types, assets, Docker, and permissions.
  • Use cases include FASTQ, BAM, and VCF processing, bioinformatics pipelines, systematic reviews of job status, and reproducible research automation.

Quick Start

Ask for help designing, configuring, or debugging a DNAnexus genomics app, data transfer task, or workflow, and provide the input files or goal you want to achieve.

Frequently Asked Questions about dnanexus-integration

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

FAQPage Schema
How do I build a DNAnexus genomics workflow using dxpy?▼

Build a DNAnexus genomics workflow by creating Python or Bash executables, configuring dxapp.json, and using the dxpy Python SDK to automate applet creation, data operations, and job execution for your bioinformatics pipelines.

What is the best way to configure dxapp.json for a DNAnexus applet?▼

Configure dxapp.json for a DNAnexus applet by defining dependencies, instance types, assets, Docker containers, and permissions to ensure your Python or Bash executable runs correctly on the platform.

Can I orchestrate parallel subjobs and chain outputs in a DNAnexus pipeline?▼

Yes, you can orchestrate parallel subjobs and chain outputs in a DNAnexus pipeline by using dxpy scripting to monitor job status, manage data records, and execute workflow steps for FASTQ, BAM, and VCF processing.

Does DNAnexus automation support uploading, downloading, and searching for genomics files?▼

DNAnexus automation supports uploading, downloading, searching, cloning, and organizing genomics files and records, enabling systematic data management and reproducible research automation across your bioinformatics workflows.

Do I need DNAnexus authentication and platform-compatible code to run bioinformatics pipelines?▼

Yes, DNAnexus authentication is required, along with platform-compatible Python or Bash execution environments, to run bioinformatics pipelines and manage workflow dependencies effectively.

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