# Dnanexus Integration

DNAnexus cloud genomics platform.

- Repository: https://github.com/synthetic-sciences/openscience (4321 stars)
- Category: Engineering
- License: Unknown
- Last updated: 2026-10-30
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add synthetic-sciences/openscience --skill dnanexus-integration -g -a claude-code -y`
Codex: `npx skills add synthetic-sciences/openscience --skill dnanexus-integration -g -a codex -y`
Cursor: `npx skills add synthetic-sciences/openscience --skill dnanexus-integration -g -a cursor -y`
Gemini CLI: `npx skills add synthetic-sciences/openscience --skill dnanexus-integration -g -a gemini-cli -y`

## Description

DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# DNAnexus Integration

## Overview

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.

## 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

### 2. Data Operations

**Purpose**: Manage files, records, and other data objects on the platform.

**Key Operations**:
- Upload/download files with `dxpy.upload_local_file()` and `dxpy.download_dxfile()`
- Create and manage records with metadata
- Search for data objects by name, properties, or type
- Clone data between projects
- Manage project folders and permissions

The rest: https://github.com/synthetic-sciences/openscience/blob/HEAD/backend/cli/skills/biology/dnanexus-integration/SKILL.md