{"id":20425017,"url":"https://github.com/databio/bedboss","last_synced_at":"2026-02-27T04:07:08.913Z","repository":{"id":163462712,"uuid":"574577670","full_name":"databio/bedboss","owner":"databio","description":"Python pipeline for processing BED files for BEDbase","archived":false,"fork":false,"pushed_at":"2026-01-29T16:15:27.000Z","size":31139,"stargazers_count":2,"open_issues_count":13,"forks_count":0,"subscribers_count":3,"default_branch":"main","last_synced_at":"2026-01-30T04:46:21.194Z","etag":null,"topics":["bed-files","bed-format","genomic-intervals","geo"],"latest_commit_sha":null,"homepage":"https://docs.bedbase.org","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-2-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/databio.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2022-12-05T16:05:37.000Z","updated_at":"2026-01-21T20:09:06.000Z","dependencies_parsed_at":null,"dependency_job_id":"d042f935-6a34-4d82-adf9-fede5bc2e531","html_url":"https://github.com/databio/bedboss","commit_stats":null,"previous_names":[],"tags_count":21,"template":false,"template_full_name":null,"purl":"pkg:github/databio/bedboss","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fbedboss","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fbedboss/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fbedboss/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fbedboss/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/databio","download_url":"https://codeload.github.com/databio/bedboss/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fbedboss/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28963559,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-01T00:42:38.011Z","status":"ssl_error","status_checked_at":"2026-02-01T00:42:35.920Z","response_time":128,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["bed-files","bed-format","genomic-intervals","geo"],"created_at":"2024-11-15T07:12:02.653Z","updated_at":"2026-02-01T01:19:41.117Z","avatar_url":"https://github.com/databio.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003ch1 align=\"center\"\u003ebedboss\u003c/h1\u003e\n\n\u003cdiv align=\"center\"\u003e\n  \n[![PEP compatible](https://pepkit.github.io/img/PEP-compatible-green.svg)](https://pep.databio.org/)\n\n[//]: # (![Run pytests]\u0026#40;https://github.com/bedbase/bedboss/workflows/Run%20instalation%20test/badge.svg\u0026#41;)\n[![pypi-badge](https://img.shields.io/pypi/v/bedboss?color=%2334D058)](https://pypi.org/project/bedboss)\n[![pypi-version](https://img.shields.io/pypi/pyversions/bedboss.svg?color=%2334D058)](https://pypi.org/project/bedboss)\n[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)\n[![Github badge](https://img.shields.io/badge/source-github-354a75?logo=github)](https://github.com/databio/bedboss)\n\n\u003c/div\u003e\n\n---\n\n**Documentation**: \u003ca href=\"https://docs.bedbase.org/bedboss\" target=\"_blank\"\u003ehttps://docs.bedbase.org/bedboss\u003c/a\u003e\n\n**Source Code**: \u003ca href=\"https://github.com/databio/bedboss\" target=\"_blank\"\u003ehttps://github.com/databio/bedboss\u003c/a\u003e\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","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Fbedboss","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatabio%2Fbedboss","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Fbedboss/lists"}