<h1 align="center">bedboss</h1>
<div align="center">
[](https://pep.databio.org/)
[](https://pypi.org/project/bedboss)
[](https://pypi.org/project/bedboss)
[](https://github.com/psf/black)
[](https://github.com/databio/bedboss)
</div>
---
**Documentation**: <a href="https://docs.bedbase.org/bedboss" target="_blank">https://docs.bedbase.org/bedboss</a>
**Source Code**: <a href="https://github.com/databio/bedboss" target="_blank">https://github.com/databio/bedboss</a>
---
BEDboss is a command-line management tool for BEDbase. It contains pipelines that filters, standardizes, and calculates statistics for genomic interval data,
functions that enters the results into a BEDbase database, deletes bed and bedsets from the database, and indexes the data to qdrant.
## Installation
To install `bedboss` use this command:
```
pip install bedboss
```
or install the latest version from the GitHub repository:
```
pip install git+https://github.com/databio/bedboss.git
```
## Development
For development, you should install all the dependencies, create a virtual environment, and work on the local database.
The workflow is described in the [development documentation](https://docs.bedbase.org/bedboss/development).
## Testing
### Requirements test:
To test requirements, install bedboss and run:
```
bedboss requirements-check
```
### Smoke tests:
Use this docs:
- [./test/README.md](./test/README.md)
## How to generate usage documentation:
Run this command in the root of the repository:
```
cd scripts
bash update_usage_docs.sh
```
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"description": "<h1 align=\"center\">bedboss</h1>\n\n<div align=\"center\">\n \n[](https://pep.databio.org/)\n\n[](https://pypi.org/project/bedboss)\n[](https://pypi.org/project/bedboss)\n[](https://github.com/psf/black)\n[](https://github.com/databio/bedboss)\n\n</div>\n\n---\n\n**Documentation**: <a href=\"https://docs.bedbase.org/bedboss\" target=\"_blank\">https://docs.bedbase.org/bedboss</a>\n\n**Source Code**: <a href=\"https://github.com/databio/bedboss\" target=\"_blank\">https://github.com/databio/bedboss</a>\n\n---\n\nBEDboss is a command-line management tool for BEDbase. It contains pipelines that filters, standardizes, and calculates statistics for genomic interval data, \nfunctions that enters the results into a BEDbase database, deletes bed and bedsets from the database, and indexes the data to qdrant.\n\n## Installation\nTo install `bedboss` use this command: \n```\npip install bedboss\n```\nor install the latest version from the GitHub repository:\n```\npip install git+https://github.com/databio/bedboss.git\n```\n\n## Development\nFor development, you should install all the dependencies, create a virtual environment, and work on the local database.\nThe workflow is described in the [development documentation](https://docs.bedbase.org/bedboss/development).\n\n\n## Testing\n\n### Requirements test:\n\nTo test requirements, install bedboss and run: \n\n```\nbedboss requirements-check\n```\n\n### Smoke tests:\n\nUse this docs:\n- [./test/README.md](./test/README.md)\n\n\n## How to generate usage documentation:\n\nRun this command in the root of the repository:\n```\ncd scripts\nbash update_usage_docs.sh\n```\n",
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