{"id":21287742,"url":"https://github.com/stjudecloud/utilities","last_synced_at":"2026-07-03T13:05:46.413Z","repository":{"id":46016778,"uuid":"298607172","full_name":"stjudecloud/utilities","owner":"stjudecloud","description":"Utility scripts created for and used on the St. Jude Cloud team.","archived":false,"fork":false,"pushed_at":"2024-04-29T15:33:30.000Z","size":124,"stargazers_count":0,"open_issues_count":5,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-10-24T01:57:22.688Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/stjudecloud.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":"CONTRIBUTING.md","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":"2020-09-25T15:11:37.000Z","updated_at":"2024-04-29T15:33:35.000Z","dependencies_parsed_at":"2024-04-29T16:46:13.847Z","dependency_job_id":"e5cef379-0083-40f7-9052-c372043171c5","html_url":"https://github.com/stjudecloud/utilities","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/stjudecloud/utilities","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Futilities","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Futilities/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Futilities/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Futilities/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/stjudecloud","download_url":"https://codeload.github.com/stjudecloud/utilities/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stjudecloud%2Futilities/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":35086558,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-07-03T02:00:05.635Z","response_time":110,"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":[],"created_at":"2024-11-21T12:15:35.630Z","updated_at":"2026-07-03T13:05:46.389Z","avatar_url":"https://github.com/stjudecloud.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# St. Jude Cloud Utilities\n\nThis repository contains an easily installable package for all of the utility scripts created for and used on the St. Jude Cloud team (broadly speaking). The repository is structured as a single package that is goverened by [`poetry`]. \n\nYou can use the snippet below to install the package and access the scripts outlined below.\n\n```bash\npip install stjudecloud-utilities\n```\n\n## Scripts\n\nThe following scripts are included in the package:\n\n### `deduplicate-feature-counts`\n\nA utility script to deduplicate St. Jude Cloud file names. Assumes files are annotated with St. Jude project names. Retains files based on the `PRIORITIES` list of prioritized projects.\n\nUsage: `dx ls /counts | deduplicate-feature-counts | bash`\n\n### `gtf-to-rseqc-bed` \n\nA utility script for converting Gencode GTFs into the custom BED12 format used by the [RSeQC software package](http://rseqc.sourceforge.net/).\n\nUsage: `gtf-to-rseqc-bed \u003cgencode gtf\u003e \u003e gencode.vFOO.bed`\n\n## Tests\n\nGiven that this repo is still new, there are no tests. When we add tests, we will update the README.\n\n## 🤝 Contributing\n\nContributions, issues and feature requests are welcome!\u003cbr /\u003eFeel free to check [issues page](https://github.com/stjudecloud/utilities/issues). You can also take a look at the [contributing guide](https://github.com/stjudecloud/utilities/blob/master/CONTRIBUTING.md).\n\n## 📝 License\n\nCopyright © 2021 [St. Jude Cloud Team](https://github.com/stjudecloud).\u003cbr /\u003e\nThis project is [MIT](https://github.com/stjudecloud/workflows/blob/master/LICENSE.md) licensed.\n\n[`poetry`]: https://python-poetry.org/docs/","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstjudecloud%2Futilities","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fstjudecloud%2Futilities","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstjudecloud%2Futilities/lists"}