{"id":23071344,"url":"https://github.com/clinical-genomics/housekeeper","last_synced_at":"2025-08-15T14:32:24.401Z","repository":{"id":52612464,"uuid":"62557211","full_name":"Clinical-Genomics/housekeeper","owner":"Clinical-Genomics","description":"File data orchestrator","archived":false,"fork":false,"pushed_at":"2024-12-09T08:54:18.000Z","size":1694,"stargazers_count":2,"open_issues_count":3,"forks_count":0,"subscribers_count":10,"default_branch":"master","last_synced_at":"2024-12-09T09:39:34.741Z","etag":null,"topics":["data","file","orchestrator"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Clinical-Genomics.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":".github/CODEOWNERS","security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2016-07-04T11:28:52.000Z","updated_at":"2024-12-09T08:54:22.000Z","dependencies_parsed_at":"2023-02-09T02:30:55.909Z","dependency_job_id":"9eb728d4-262c-4278-8305-d15546caf7ab","html_url":"https://github.com/Clinical-Genomics/housekeeper","commit_stats":{"total_commits":472,"total_committers":16,"mean_commits":29.5,"dds":0.2860169491525424,"last_synced_commit":"9e98a7d04d504627acc251397b11ba9aee176558"},"previous_names":[],"tags_count":119,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Clinical-Genomics%2Fhousekeeper","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Clinical-Genomics%2Fhousekeeper/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Clinical-Genomics%2Fhousekeeper/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Clinical-Genomics%2Fhousekeeper/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Clinical-Genomics","download_url":"https://codeload.github.com/Clinical-Genomics/housekeeper/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":229920920,"owners_count":18144863,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":["data","file","orchestrator"],"created_at":"2024-12-16T07:13:40.053Z","updated_at":"2024-12-16T07:13:43.004Z","avatar_url":"https://github.com/Clinical-Genomics.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Housekeeper\n![Housekeeper tests][github-url] [![Coverage Status][coveralls-image]][coveralls-url] [![CodeFactor][codefactor-image]][codefactor-url] [![Code style: black][black-image]][black-url]\n\n### Store, tag, fetch, and archive files with ease 🗃\n\n**Housekeeper** is a tool that aims to provide:\n\n- a backend for storing versioned bundles of files\n- different interfaces (Python, CLI, REST) for fetching files based on tags\n- a way to backup and retrieve bundles from long-term storage\n\n## Installation\n\nHousekeeper written in Python 3.6+ and is available on the [Python Package Index][pypi] (PyPI).\n\n```bash\npoetry install\n```\n\nIf you would like to install the latest development version:\n\n```bash\ngit clone https://github.com/Clinical-Genomics/housekeeper\ncd housekeeper\npoetry install\n```\n\n## Contributing\n\nHousekeeper is using GitHub flow branching model as described in our [development manual][development manual].\n\n## Documentation\n\n### Command line interface\n\n#### Config file\n\nHousekeeper supports a basic YAML config. The following options are supported:\n\n```yaml\n---\ndatabase: mysql+pymysql://userName:passWord@domain.com/database\nroot: /path/to/root/dir\n```\n\nThe `root` option is used to store files within the Housekeeper context.\n\n#### Command: `init`\n\nSetup (or reset) the database. It will simply setup all the tables in the database. You can reset an existing database by using the `--reset` option.\n\n```bash\nhousekeeper --database \"sqlite:///hk.sqlite3\" init\nSuccess! New tables: bundle, file, file_tag_link, tag, version\n```\n\n#### Command: `include`\n\nInclude (hard-link) all files of an existing bundle version into Housekeeper and the `root` path.\n\n```bash\nhousekeeper myBundle\n```\n\nThis will only work if the bundle only has a single version which can be \"imported\". If you want to import a specific version of a bundle you can use the `--version` option.\n\n#### Command: `delete files`\n\nDelete files that are not on disk anymore like his:\n`housekeeper delete files --tag fastq --notondisk`\n\nRemove all bam files before a certain date:\n`housekeeper delete files --tag bam --before 2017-06-15`\n\nRemove fastq files from a flowcell:\n`housekeeper delete files --tag fastq --tag H0HKKALXX`\n\nIt'll always ask for confirmation, unless you add --yes:\n`housekeeper delete files --bundle sillyfish --yes`\n\nIf you do not provide a --tag or --bundle, essentially deleting everything, the function will not let you do that.\n\n[pypi]: https://pypi.python.org/pypi/housekeeper/\n[coveralls-url]: https://coveralls.io/r/Clinical-Genomics/housekeeper\n[coveralls-image]: https://img.shields.io/coveralls/Clinical-Genomics/housekeeper.svg?style=flat-square\n[github-url]: https://github.com/Clinical-Genomics/housekeeper/workflows/Housekeeper%20tests/badge.svg\n[development manual]: http://www.clinicalgenomics.se/development/dev/githubflow/\n[codefactor-image]: https://www.codefactor.io/repository/github/clinical-genomics/housekeeper/badge\n[codefactor-url]: https://www.codefactor.io/repository/github/clinical-genomics/housekeeper\n[black-image]: https://img.shields.io/badge/code%20style-black-000000.svg\n[black-url]: https://github.com/psf/black","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fclinical-genomics%2Fhousekeeper","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fclinical-genomics%2Fhousekeeper","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fclinical-genomics%2Fhousekeeper/lists"}