adthrasher / cloud-app-tutorial

Application tutorials for St. Jude Cloud.

St. Jude App Tutorial

This repository contains the example app tutorials that demonstrate how to manipulate and work with the data requested from the St. Jude Cloud Platform. The examples hosted in this repository are meant to serve as a starting point for developing your own application.

Documentation

For more information on how to request and access datasets and how to write apps and tools to manipulate data in the cloud, refer to the St. Jude Cloud Documentation.

This repository hosts the example tutorial applications located in the Data Guides > Creating a Cloud Application section.

Requirements

For accessing St. Jude next generation sequencing data and writing cloud applications, you will need a DNAnexus account and dx-toolkit. To explore or manage datasets, refer to our guide Working with Our Data.

Apps

• dx-adapter-trim - Example application that uses cutadapt to trim sequencing adapters. This app demonstrates providing data to the app via the resources directory. Note this should primarily be used for small, app-specific resources.
• dx-bam-to-fastq - Example application that extracts FastQ files from aligned BAMs. This app demonstrates returning an array of files as output.
• dx-bwa-mem - Example application that aligns FastQ files to a reference genome using BWA-MEM. Demonstrates pulling reference files from the common St. Jude Cloud Reference Data project dynamically based on user input for use in the application.
• dx-fastqc-example-app - Example application used in the Data Guides > Creating a Cloud Application section of the St. Jude Cloud documentation.

Feedback

This repository is still currently under construction. If you have any additional questions, be sure to contact us!

References

For more information, visit:

• St. Jude Cloud
• St. Jude Cloud Documentation
• DNAnexus Wiki

License

• Apache License 2.0