How does it handle DNAnexus app configuration?

It provides patterns for writing dxapp.json files, managing system dependencies (execDepends), and integrating Docker containers for complex environments.

Does this skill help with dxpy scripts?

Yes, it includes detailed reference documentation and code examples for using the dxpy Python SDK to automate data uploads, job execution, and project management.

Is local authentication required?

Yes, users should perform 'dx login' on their terminal; this skill then provides the necessary commands to verify the session and interact with the platform.

Can I use this for bioinformatics pipeline development?

Absolutely. The skill is designed to assist in creating apps for alignment, variant calling, and processing common file formats like FASTQ, BAM, and VCF.

What is the DNAnexus Integration skill?

It is a specialized capability for Claude that provides guidance, code patterns, and best practices for developing and managing apps on the DNAnexus cloud genomics platform.

DNAnexus Integration

Name: DNAnexus Integration
Author: BbgnsurfTech

byBbgnsurfTech

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데이터 과학 및 ML

Integrates Claude with the DNAnexus cloud platform to develop, deploy, and manage genomics pipelines and biomedical data analyses.

소개

This skill empowers bioinformaticians and developers to interact seamlessly with the DNAnexus cloud genomics platform using the dxpy Python SDK. It provides comprehensive support for the entire development lifecycle, from generating applet skeletons and managing large-scale genomic data objects like FASTQ, BAM, and VCF files to orchestrating complex workflows and monitoring parallel job execution. By streamlining the configuration of dxapp.json and handling platform-specific implementation patterns, it simplifies the transition from local bioinformatics scripts to scalable, production-grade cloud pipelines.

주요 기능

Advanced workflow orchestration and parallel job monitoring capabilities
3 GitHub stars
Configuration support for dxapp.json, system dependencies, and Docker
Comprehensive genomic data management using the dxpy Python SDK
Automated DNAnexus app/applet skeleton generation and deployment patterns
Standardized patterns for processing FASTQ, BAM, and VCF files

사용 사례

Orchestrating multi-step analysis workflows across large sequencing cohorts
Automating bulk genomic data uploads and systematic metadata tagging
Building and deploying scalable bioinformatics pipelines for variant calling

소개

주요 기능

Advanced workflow orchestration and parallel job monitoring capabilities
3 GitHub stars
Configuration support for dxapp.json, system dependencies, and Docker
Comprehensive genomic data management using the dxpy Python SDK
Automated DNAnexus app/applet skeleton generation and deployment patterns
Standardized patterns for processing FASTQ, BAM, and VCF files

사용 사례

Orchestrating multi-step analysis workflows across large sequencing cohorts
Automating bulk genomic data uploads and systematic metadata tagging
Building and deploying scalable bioinformatics pipelines for variant calling