https://github.com/databio/bedboss

Python pipeline for processing BED files for BEDbase
https://github.com/databio/bedboss

bed-files bed-format genomic-intervals geo

Last synced: 3 months ago
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Python pipeline for processing BED files for BEDbase

• Host: GitHub
• URL: https://github.com/databio/bedboss
• Owner: databio
• License: bsd-2-clause
• Created: 2022-12-05T16:05:37.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2026-01-29T16:15:27.000Z (4 months ago)
• Last Synced: 2026-01-30T04:46:21.194Z (4 months ago)
• Topics: bed-files, bed-format, genomic-intervals, geo
• Language: Python
• Homepage: https://docs.bedbase.org
• Size: 29.7 MB
• Stars: 2
• Watchers: 3
• Forks: 0
• Open Issues: 13
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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---

**Documentation**: https://docs.bedbase.org/bedboss

**Source Code**: https://github.com/databio/bedboss

---

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

```