Does it support standard genomics file formats?

Absolutely; it is specifically designed to handle common formats like FASTQ, BAM, and VCF files through the platform's native data management features.

Do I need to have the DNAnexus SDK installed to use this skill?

Yes, you should have the dxpy library installed and be authenticated via the 'dx login' command to utilize the full capabilities of this integration.

How does this skill assist with workflow orchestration?

It provides patterns for chaining jobs together, using output references from one job as inputs for the next, and managing parallel subjob execution.

Can this skill help with configuring complex app dependencies?

Yes, it includes detailed guidance on writing dxapp.json files, managing execDepends, and integrating Docker containers for specialized bioinformatics tools.

What is the primary purpose of the DNAnexus Integration skill?

It provides a specialized environment for building, managing, and executing genomics pipelines and data operations on the DNAnexus cloud platform using the dxpy SDK.

DNAnexus Integration

Name: DNAnexus Integration
Author: Microck

byMicrock

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Cloud Infrastructure

Simplifies genomics pipeline development and biomedical data management on the DNAnexus cloud platform.

About

This skill empowers researchers and bioinformaticians to interact seamlessly with the DNAnexus platform directly through Claude, facilitating the creation, deployment, and management of cloud-based genomics apps and workflows. It provides comprehensive support for the dxpy Python SDK, managing complex data objects like FASTQ and BAM files, and automating job execution and monitoring. Whether you are configuring dxapp.json specifications or orchestrating multi-step bioinformatics pipelines, this skill provides the structural patterns and best practices needed for efficient biomedical data analysis in a cloud-native environment.

Key Features

81 GitHub stars
Streamlined app and applet development lifecycle from skeleton to deployment
Comprehensive data management for genomics files, records, and metadata
Advanced dxpy Python SDK integration for programmatic platform control
Standardized configuration for dxapp.json, Docker, and system dependencies
Automated job execution, monitoring, and workflow orchestration patterns

Use Cases

Orchestrating complex, multi-stage analysis workflows across cloud resources
Automating large-scale data uploads and organization for genomic research projects
Developing and deploying custom bioinformatics tools for sequence alignment or variant calling

About

Key Features

81 GitHub stars
Streamlined app and applet development lifecycle from skeleton to deployment
Comprehensive data management for genomics files, records, and metadata
Advanced dxpy Python SDK integration for programmatic platform control
Standardized configuration for dxapp.json, Docker, and system dependencies
Automated job execution, monitoring, and workflow orchestration patterns

Use Cases

Orchestrating complex, multi-stage analysis workflows across cloud resources
Automating large-scale data uploads and organization for genomic research projects
Developing and deploying custom bioinformatics tools for sequence alignment or variant calling