https://github.com/stjudecloud/utilities
Utility scripts created for and used on the St. Jude Cloud team.
https://github.com/stjudecloud/utilities
Last synced: 3 days ago
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Utility scripts created for and used on the St. Jude Cloud team.
- Host: GitHub
- URL: https://github.com/stjudecloud/utilities
- Owner: stjudecloud
- License: mit
- Created: 2020-09-25T15:11:37.000Z (almost 6 years ago)
- Default Branch: main
- Last Pushed: 2024-04-29T15:33:30.000Z (about 2 years ago)
- Last Synced: 2025-10-24T01:57:22.688Z (9 months ago)
- Language: Python
- Homepage:
- Size: 121 KB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
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README
# St. Jude Cloud Utilities
This 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`].
You can use the snippet below to install the package and access the scripts outlined below.
```bash
pip install stjudecloud-utilities
```
## Scripts
The following scripts are included in the package:
### `deduplicate-feature-counts`
A 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.
Usage: `dx ls /counts | deduplicate-feature-counts | bash`
### `gtf-to-rseqc-bed`
A utility script for converting Gencode GTFs into the custom BED12 format used by the [RSeQC software package](http://rseqc.sourceforge.net/).
Usage: `gtf-to-rseqc-bed > gencode.vFOO.bed`
## Tests
Given that this repo is still new, there are no tests. When we add tests, we will update the README.
## 🤝 Contributing
Contributions, issues and feature requests are welcome!
Feel 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).
## 📝 License
Copyright © 2021 [St. Jude Cloud Team](https://github.com/stjudecloud).
This project is [MIT](https://github.com/stjudecloud/workflows/blob/master/LICENSE.md) licensed.
[`poetry`]: https://python-poetry.org/docs/