bedboss

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.

Testing

Requirements test:

To test requirements, install bedboss and run:

bedboss requirements-check

Smoke tests:

Use this docs:

• ./test/README.md

How to generate usage documentation:

Run this command in the root of the repository:

cd scripts
bash update_usage_docs.sh