Can I manage bioinformatics files like FASTQ or VCF with this skill?

Absolutely. The skill includes core capabilities for uploading, downloading, searching, and organizing all types of genomic data objects.

How does this skill help with app deployment?

It assists in creating app skeletons, configuring dxapp.json, managing dependencies (including Docker), and executing deployment commands like 'dx build'.

Does this skill support the dxpy Python SDK?

Yes, it provides detailed guidance and implementation patterns for using the dxpy library for programmatic platform access and automation.

What is the primary use of the DNAnexus Integration skill?

It is used to build, deploy, and manage genomics applications and data on the DNAnexus cloud platform directly through Claude Code's interface.

Can I monitor running jobs or workflows?

Yes, the skill provides patterns for launching jobs, monitoring execution status, and handling subjobs for parallel processing.

DNAnexus Genomics Integration

Name: DNAnexus Genomics Integration
Author: jimmc414

byjimmc414

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324

Data Science & ML

Streamlines the development, deployment, and management of bioinformatics pipelines and data on the DNAnexus cloud genomics platform.

About

This skill empowers Claude to interact natively with the DNAnexus platform, a leading environment for biomedical data analysis and genomics. It provides comprehensive support for building and deploying apps and applets, managing large-scale genomic data objects such as FASTQ, BAM, and VCF files, orchestrating complex workflows, and utilizing the dxpy Python SDK for automated pipeline execution. Whether you are configuring dxapp.json specifications, managing cloud project permissions, or monitoring parallel job executions, this skill ensures Claude adheres to domain-specific best practices for high-performance cloud bioinformatics.

Key Features

Job orchestration and monitoring for multi-step analysis workflows
Full Python SDK (dxpy) integration for programmatic platform interaction
Comprehensive data lifecycle management for genomic files and records
Automated DNAnexus app/applet skeleton generation and deployment patterns
324 GitHub stars
Dependency management including Docker integration and resource configuration

Use Cases

Automating batch processing and parallel execution of genomic analyses
Managing and searching large-scale sequencing datasets across cloud projects
Building and deploying custom variant calling or sequence alignment pipelines

About

Key Features

Job orchestration and monitoring for multi-step analysis workflows
Full Python SDK (dxpy) integration for programmatic platform interaction
Comprehensive data lifecycle management for genomic files and records
Automated DNAnexus app/applet skeleton generation and deployment patterns
324 GitHub stars
Dependency management including Docker integration and resource configuration

Use Cases

Automating batch processing and parallel execution of genomic analyses
Managing and searching large-scale sequencing datasets across cloud projects
Building and deploying custom variant calling or sequence alignment pipelines