What is the primary purpose of this DNAnexus skill?

It provides Claude with the specialized knowledge to build apps, manage data, and automate bioinformatics workflows on the DNAnexus cloud platform.

Does this skill support the dxpy Python SDK?

Yes, it includes comprehensive patterns and best practices for using the dxpy SDK to interact with DNAnexus resources programmatically.

How does it help with app development on DNAnexus?

It provides guidance on using dx-app-wizard, writing entry points, configuring dxapp.json, and managing dependencies or Docker containers.

Can I use this to manage large genomic files?

Absolutely. It covers operations for handling FASTQ, BAM, VCF, and other bioinformatics data types, including uploading, downloading, and searching.

Is this skill useful for batch processing?

Yes, it includes specific patterns for parallel job execution and multi-step pipeline chaining to handle large-scale datasets efficiently.

DNAnexus Integration

Name: DNAnexus Integration
Author: K-Dense-AI

byK-Dense-AI

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2,188

Data Science & ML

Streamlines biomedical data management and genomics workflow automation on the DNAnexus cloud platform.

About

This skill empowers Claude to interact seamlessly with the DNAnexus cloud genomics platform, facilitating the end-to-end lifecycle of biomedical data analysis. It provides specialized knowledge for building and deploying apps/applets, managing large-scale genomic data files like FASTQ and VCF, orchestrating complex workflows, and utilizing the dxpy Python SDK for automation. Whether you are setting up bioinformatics pipelines, managing project permissions, or monitoring job execution, this skill provides the implementation patterns and best practices needed to navigate the DNAnexus ecosystem efficiently.

Key Features

App & Applet Development: Build, deploy, and test DNAnexus executables with proper entry points and skeletons.
dxpy Python SDK Support: Implement programmatic automation using high-level data object handlers and API calls.
Configuration Management: Define dependencies, system packages, and Docker integrations via dxapp.json.
Workflow Orchestration: Launch jobs, create subjobs for parallel processing, and chain multi-step analysis pipelines.
2,188 GitHub stars
Genomic Data Management: Upload, download, search, and organize sequencing data and analysis records.

Use Cases

Building a variant calling pipeline using standard bioinformatics tools within a DNAnexus applet.
Automating the batch processing of hundreds of FASTQ files from a specific sequencing run.
Managing and organizing bioinformatics results across multiple projects with systematic metadata tagging.

About

Key Features

App & Applet Development: Build, deploy, and test DNAnexus executables with proper entry points and skeletons.
dxpy Python SDK Support: Implement programmatic automation using high-level data object handlers and API calls.
Configuration Management: Define dependencies, system packages, and Docker integrations via dxapp.json.
Workflow Orchestration: Launch jobs, create subjobs for parallel processing, and chain multi-step analysis pipelines.
2,188 GitHub stars
Genomic Data Management: Upload, download, search, and organize sequencing data and analysis records.

Use Cases

Building a variant calling pipeline using standard bioinformatics tools within a DNAnexus applet.
Automating the batch processing of hundreds of FASTQ files from a specific sequencing run.
Managing and organizing bioinformatics results across multiple projects with systematic metadata tagging.