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DNAnexus Integration

Maintainer K-Dense Inc. · Last updated April 1, 2026

DNAnexus is a cloud platform for biomedical data analysis and genomics. Build and deploy apps/applets, manage data objects, run workflows, and use the dxpy Python SDK for genomics pipeline development and execution.

Claude CodeOpenClawNanoClawAnalysisReproductiondnanexus-integrationcloud-biomedintegrationcloud platforms for genomics & biomedical data

Original source

K-Dense-AI/claude-scientific-skills

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/dnanexus-integration

Maintainer
K-Dense Inc.
License
Unknown
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • DNAnexus is a cloud platform for biomedical data analysis and genomics. Build and deploy apps/applets, manage data objects, run workflows, and use the dxpy Python SDK for genomics pipeline development and execution.
  • input_file = dxpy.upload_local_file("sample.fastq", project="project-xxxx").

Source Doc

Excerpt From SKILL.md

When to Use This Skill

This skill should be used when:

  • Creating, building, or modifying DNAnexus apps/applets
  • Uploading, downloading, searching, or organizing files and records
  • Running analyses, monitoring jobs, creating workflows
  • Writing scripts using dxpy to interact with the platform
  • Setting up dxapp.json, managing dependencies, using Docker
  • Processing FASTQ, BAM, VCF, or other bioinformatics files
  • Managing projects, permissions, or platform resources

Core Capabilities

The skill is organized into five main areas, each with detailed reference documentation:

1. App Development

Purpose: Create executable programs (apps/applets) that run on the DNAnexus platform.

Key Operations:

  • Generate app skeleton with dx-app-wizard
  • Write Python or Bash apps with proper entry points
  • Handle input/output data objects
  • Deploy with dx build or dx build --app
  • Test apps on the platform

Common Use Cases:

  • Bioinformatics pipelines (alignment, variant calling)
  • Data processing workflows
  • Quality control and filtering
  • Format conversion tools

Reference: See references/app-development.md for:

  • Complete app structure and patterns
  • Python entry point decorators
  • Input/output handling with dxpy
  • Development best practices
  • Common issues and solutions

Use cases

  • Creating, building, or modifying DNAnexus apps/applets.
  • Uploading, downloading, searching, or organi.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

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