What is the DNAnexus Integration skill?

It is a specialized capability for Claude Code that provides deep knowledge and implementation patterns for interacting with the DNAnexus cloud genomics platform.

How does this skill help with dependency management?

It provides guidance on managing system packages through execDepends, bundling custom tools, and integrating Docker containers within the DNAnexus environment.

Can I use this skill to build bioinformatics apps?

Absolutely. The skill covers the entire development lifecycle, from creating the app skeleton with dx-app-wizard to configuring dxapp.json and deploying with dx build.

Does it support complex genomic file formats?

Yes, it is designed to handle common bioinformatics formats such as FASTQ, BAM, and VCF, including patterns for their processing and storage.

Does this skill support the dxpy Python SDK?

Yes, it includes detailed documentation and code examples for using the dxpy SDK to manage data, launch jobs, and interact with the platform programmatically.

DNAnexus Genomics Integration

Name: DNAnexus Genomics Integration
Author: Zehong-Wang

byZehong-Wang

0•

Data Science & ML

Streamlines genomic data management and bioinformatics app development on the DNAnexus cloud platform using the dxpy Python SDK.

This skill equips Claude with specialized knowledge for the DNAnexus cloud genomics platform, enabling it to assist in building, deploying, and managing complex bioinformatics workflows. It provides domain-specific guidance for the dxpy Python SDK, data object management for sequencing files (FASTQ, BAM, VCF), and the configuration of apps and applets via dxapp.json. Whether you are automating large-scale data uploads, orchestrating multi-step analysis pipelines, or debugging cloud job executions, this skill offers the patterns and best practices needed for efficient cloud-based biomedical research.

Key Features

01Advanced configuration management for Docker integration and system dependencies

02Detailed reference for the dxpy Python SDK and high-level platform utilities

03Comprehensive data management for genomic files, records, and metadata

04End-to-end app and applet development including skeleton generation and deployment

05Job execution and workflow orchestration with parallel processing patterns

060 GitHub stars

Use Cases

01Chaining multiple analysis steps into a robust, cloud-based production pipeline

02Developing and deploying custom bioinformatics tools as scalable DNAnexus apps

03Automating the upload and systematic organization of high-throughput sequencing data

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add zehong-wang/kosmos dnanexus-integration

For use in Claude.ai and ChatGPT

Download Skill