{"id":21287766,"url":"https://github.com/stjudecloud/cloud-app-tutorial","last_synced_at":"2026-02-11T12:10:04.882Z","repository":{"id":115471401,"uuid":"171346471","full_name":"stjudecloud/cloud-app-tutorial","owner":"stjudecloud","description":"Cloud application examples for St. Jude Cloud.","archived":false,"fork":false,"pushed_at":"2020-05-04T14:08:01.000Z","size":9774,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-03-15T15:31:37.566Z","etag":null,"topics":["cloud","documentation","genomics","stjudecloud","tutorial","workflow","workflow-engine"],"latest_commit_sha":null,"homepage":"https://stjude.cloud/docs/guides/genomics-platform/analyzing-data/creating-a-cloud-app/","language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/stjudecloud.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-02-18T19:50:53.000Z","updated_at":"2021-03-24T18:42:31.000Z","dependencies_parsed_at":"2023-12-04T23:30:18.834Z","dependency_job_id":null,"html_url":"https://github.com/stjudecloud/cloud-app-tutorial","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/stjudecloud/cloud-app-tutorial","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Fcloud-app-tutorial","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Fcloud-app-tutorial/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Fcloud-app-tutorial/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Fcloud-app-tutorial/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/stjudecloud","download_url":"https://codeload.github.com/stjudecloud/cloud-app-tutorial/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Fcloud-app-tutorial/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":272140192,"owners_count":24880458,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-08-25T02:00:12.092Z","response_time":1107,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["cloud","documentation","genomics","stjudecloud","tutorial","workflow","workflow-engine"],"created_at":"2024-11-21T12:15:40.540Z","updated_at":"2026-02-11T12:09:59.846Z","avatar_url":"https://github.com/stjudecloud.png","language":null,"readme":"# St. Jude App Tutorial\n\nThis 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.\n\n## Documentation\n\nFor 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/).\n\nThis repository hosts the example tutorial applications located in the [Data Guides \u003e Creating a Cloud Application](https://www.stjude.cloud/docs/guides/data/creating-a-cloud-app/) section.\n\n## Requirements\n\nFor 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/).\n\n## Apps\n\n* `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.\n* `dx-bam-to-fastq` - Example application that extracts FastQ files from aligned BAMs. This app demonstrates returning an array of files as output.\n* `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.\n* `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.\n* `dx-fastqc-example-app` - Example application used in the [Data Guides \u003e Creating a Cloud Application](https://www.stjude.cloud/docs/guides/data/creating-a-cloud-app/) section of the St. Jude Cloud documentation.\n\n## Feedback\n\nThis 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/)!\n\n## References\n\nFor more information, visit:\n* [St. Jude Cloud](https://www.stjude.cloud/)\n* [St. Jude Cloud Documentation](https://www.stjude.cloud/docs/)\n* [DNAnexus Wiki](https://documentation.dnanexus.com/)\n\n## License\n\n* [Apache License 2.0](./LICENSE)\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstjudecloud%2Fcloud-app-tutorial","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fstjudecloud%2Fcloud-app-tutorial","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstjudecloud%2Fcloud-app-tutorial/lists"}