dnanexus-integration

Topics in the source

• DNAnexus Integration
• Overview
• When to Use This Skill
• Core Capabilities
• 1. App Development
• 2. Data Operations
• 3. Job Execution
• 4. Python SDK (dxpy)

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

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