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dnanexus-integration

Interact with the DNAnexus cloud genomics platform using the Python SDK.

1|Updated Jan 14, 2026
Search Tags:#bioinformatics#genomics#pipeline#cloud computing#dxpy#dnanexus
One-click install
npx skills add https://github.com/Sologa/codex-pipeline --skill dnanexus-integration-sologa
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: dnanexus-integration
Source: https://github.com/Sologa/codex-pipeline/tree/main/.codex/skills/dnanexus-integration
Command: npx skills add https://github.com/Sologa/codex-pipeline --skill dnanexus-integration-sologa

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides comprehensive tools and guidance for interacting with the DNAnexus cloud genomics platform, enabling efficient development, data management, and execution of bioinformatics pipelines.

Core Features & Use Cases

  • App Development: Build and deploy custom apps/applets using Python or Bash.
  • Data Operations: Upload, download, search, and manage files and records.
  • Job Execution: Run analyses, monitor jobs, and orchestrate complex workflows.
  • Python SDK (dxpy): Programmatically control the platform.
  • Configuration: Define app dependencies and execution environments.
  • Use Case: A researcher needs to process FASTQ files from a new sequencing run, align them to a reference genome using a custom applet, and then call variants, all orchestrated through DNAnexus.

Quick Start

Use the dnanexus-integration skill to upload a local file named 'sample.fastq' to your DNAnexus project 'project-xxxx'.

Frequently Asked Questions about dnanexus-integration

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

FAQPage Schema
How do I use dxpy to upload files and manage data on the DNAnexus platform?▼

You can use the dxpy Python SDK to programmatically upload, download, search, and manage files and records on the DNAnexus cloud genomics platform. This Skill provides guidance for these data operations.

How do I build and deploy custom bioinformatics apps on DNAnexus?▼

Building custom DNAnexus apps is supported by defining app dependencies and execution environments. You can develop and deploy custom applets using Python or Bash through this Skill's guidance.

Can I orchestrate complex genomics workflows and monitor job execution on DNAnexus?▼

Yes, you can run analyses, monitor jobs, and orchestrate complex genomics workflows on the DNAnexus platform. This Skill facilitates job execution and workflow orchestration for bioinformatics pipelines.

Do I need a DNAnexus account and dxpy installation to execute genomics pipelines?▼

Yes, a DNAnexus account and dxpy installation are required for programmatic access. These prerequisites enable you to control the cloud genomics platform and execute bioinformatics workflows.

What is the best way to process FASTQ files and call variants using cloud computing?▼

Using DNAnexus cloud computing, you can process FASTQ files, align them to a reference genome using a custom applet, and call variants. This Skill guides orchestrating such bioinformatics workflows.

Why does my DNAnexus applet configuration fail to define execution environments correctly?▼

Configuring DNAnexus applets requires properly defining app dependencies and execution environments. This Skill provides configuration management guidance to ensure your app development and execution setup is correct.

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