Does this skill help with managing genomics files?

Yes, it provides specific patterns for handling large-scale data objects including FASTQ, BAM, and VCF files, as well as searching and organizing metadata records.

Does it support parallel processing patterns?

Yes, the skill includes patterns for batch processing and launching parallel subjobs to handle multiple genomic samples simultaneously.

Can I use this for configuring app dependencies?

Absolutely. It includes detailed guidance on writing dxapp.json files, managing system dependencies, and integrating Docker containers.

What is the primary use of the DNAnexus Integration skill?

It is designed to help developers build, deploy, and manage bioinformatics applications and data workflows on the DNAnexus cloud platform using the dxpy SDK.

How does it assist with the dxpy Python SDK?

It provides a comprehensive reference for dxpy classes and functions, error handling patterns, and high-level utilities for platform interaction.

DNAnexus Integration

Name: DNAnexus Integration
Author: Activer007

byActiver007

•

データサイエンスとML

Streamlines bioinformatics pipeline development and genomics data management on the DNAnexus cloud platform.

概要

This skill provides a comprehensive toolkit for developers working within the DNAnexus ecosystem, enabling seamless creation, deployment, and management of genomics workflows. It offers domain-specific guidance for using the dxpy Python SDK, building apps and applets, and managing large-scale biological data objects like FASTQ, BAM, and VCF files. By providing standardized implementation patterns for job orchestration, dependency management via dxapp.json, and data lifecycle operations, it significantly accelerates the development of production-grade bioinformatics pipelines on specialized cloud infrastructure.

主な機能

1 GitHub stars
Advanced genomics data management for sequencing files and metadata records
Programmatic platform access via comprehensive dxpy SDK patterns
Full lifecycle app development using dx-app-wizard and dxpy decorators
Automated job execution and multi-step workflow orchestration
Containerized environment configuration with Docker and dxapp.json

ユースケース

Building and deploying custom variant calling or alignment applets to the cloud
Monitoring and debugging large-scale parallel processing jobs across genomic samples
Automating high-throughput sequencing data uploads and project organization

概要

主な機能

1 GitHub stars
Advanced genomics data management for sequencing files and metadata records
Programmatic platform access via comprehensive dxpy SDK patterns
Full lifecycle app development using dx-app-wizard and dxpy decorators
Automated job execution and multi-step workflow orchestration
Containerized environment configuration with Docker and dxapp.json

ユースケース

Building and deploying custom variant calling or alignment applets to the cloud
Monitoring and debugging large-scale parallel processing jobs across genomic samples
Automating high-throughput sequencing data uploads and project organization