https://github.com/stjudecloud/cloud-app-tutorial
Cloud application examples for St. Jude Cloud.
https://github.com/stjudecloud/cloud-app-tutorial
cloud documentation genomics stjudecloud tutorial workflow workflow-engine
Last synced: 5 months ago
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Cloud application examples for St. Jude Cloud.
- Host: GitHub
- URL: https://github.com/stjudecloud/cloud-app-tutorial
- Owner: stjudecloud
- License: apache-2.0
- Created: 2019-02-18T19:50:53.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2020-05-04T14:08:01.000Z (over 5 years ago)
- Last Synced: 2025-03-15T15:31:37.566Z (11 months ago)
- Topics: cloud, documentation, genomics, stjudecloud, tutorial, workflow, workflow-engine
- Homepage: https://stjude.cloud/docs/guides/genomics-platform/analyzing-data/creating-a-cloud-app/
- Size: 9.32 MB
- Stars: 1
- Watchers: 4
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# 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](https://www.stjude.cloud/). 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](https://www.stjude.cloud/docs/).
This repository hosts the example tutorial applications located in the [Data Guides > Creating a Cloud Application](https://www.stjude.cloud/docs/guides/data/creating-a-cloud-app/) section.
## Requirements
For accessing St. Jude next generation sequencing data and writing cloud applications, you will need a [DNAnexus account](https://www.stjude.cloud/docs/create-an-account/) and [dx-toolkit](https://wiki.dnanexus.com/downloads). To explore or manage datasets, refer to our guide [Working with Our Data](https://www.stjude.cloud/docs/guides/data/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-cwl-alignment` - Example application that aligns FastQ files to a reference genome, sorts the resulting BAM, indexes the BAM, and then produces a flagstat. The pipeline is orchestrated using CWL. The CWL workflow is run in parallel on a single node using multiple cores.
* `dx-fastqc-example-app` - Example application used in the [Data Guides > Creating a Cloud Application](https://www.stjude.cloud/docs/guides/data/creating-a-cloud-app/) 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](https://hospital.stjude.org/apps/forms/fb/st-jude-cloud-contact/)!
## References
For more information, visit:
* [St. Jude Cloud](https://www.stjude.cloud/)
* [St. Jude Cloud Documentation](https://www.stjude.cloud/docs/)
* [DNAnexus Wiki](https://documentation.dnanexus.com/)
## License
* [Apache License 2.0](./LICENSE)