Can I use Docker with this integration?

Yes, the skill covers how to integrate Docker containers and manage dependencies within the DNAnexus app configuration.

How does it handle job monitoring?

The skill provides patterns for launching jobs, tracking their status, retrieving logs, and managing parallel execution threads.

DNAnexus is a secure, cloud-based platform designed specifically for the storage, management, and analysis of biomedical data and genomics research.

Can this skill help with dxpy Python scripts?

Yes, it provides detailed implementation patterns, class references, and error-handling strategies for the dxpy Python SDK.

Does it support bioinformatics file formats?

Absolutely. It includes specific guidance for processing common genomic formats such as FASTQ, BAM, and VCF files.

DNAnexus Genomics Integration

Name: DNAnexus Genomics Integration
Author: Microck

byMicrock

•

数据科学与机器学习

Streamlines biomedical data analysis and genomics pipeline development on the DNAnexus cloud platform.

关于

This skill empowers developers to seamlessly build, deploy, and manage cloud-native genomics applications and workflows within the DNAnexus ecosystem. It provides comprehensive guidance for the dxpy Python SDK, file management of large-scale biological datasets like FASTQ and VCF, and the orchestration of complex bioinformatics pipelines. By integrating these capabilities, users can automate data operations, monitor distributed job execution, and optimize resource configuration while adhering to platform-specific best practices.

主要功能

89 GitHub stars
End-to-end app and applet development using the dxpy Python SDK
Automated data operations for uploading, downloading, and searching genomics files
Sophisticated job execution and multi-step workflow orchestration
Advanced configuration management via dxapp.json and Docker integration
Detailed reference patterns for parallel processing and subjob creation

使用场景

Automating the migration and organization of massive biomedical datasets across cloud projects
Monitoring and debugging complex distributed analysis jobs in a production environment
Building and deploying scalable bioinformatics pipelines for sequence alignment and variant calling

关于

主要功能

89 GitHub stars
End-to-end app and applet development using the dxpy Python SDK
Automated data operations for uploading, downloading, and searching genomics files
Sophisticated job execution and multi-step workflow orchestration
Advanced configuration management via dxapp.json and Docker integration
Detailed reference patterns for parallel processing and subjob creation

使用场景

Automating the migration and organization of massive biomedical datasets across cloud projects
Monitoring and debugging complex distributed analysis jobs in a production environment
Building and deploying scalable bioinformatics pipelines for sequence alignment and variant calling