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        "author": "Robin Andeer",
        "author_email": "robin.andeer@scilifelab.se",
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            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.7",
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            "Programming Language :: Python :: 3.3",
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        "description": "# Housekeeper [![Build Status][travis-image]][travis-url] [![Coverage Status][coveralls-image]][coveralls-url]\n\n### Store, tag, fetch, and archive files with ease \ud83d\uddc3\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### Todo\n\n- [ ] re-implement the archive/encryption interface [@ingkebil]\n- [ ] handle clean up of expired bundles [@robinandeer]\n- [ ] expand the CLI with `get` command etc. [@robinandeer]\n\n## Installation\n\nHousekeeper written in Python 3.6+ and is available on the [Python Package Index][pypi] (PyPI).\n\n```bash\npip install housekeeper\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\npip install --editable .\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 very simple 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[travis-url]: https://travis-ci.org/Clinical-Genomics/housekeeper\n[travis-image]: https://img.shields.io/travis/Clinical-Genomics/housekeeper.svg?style=flat-square\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[development manual]: http://www.clinicalgenomics.se/development/dev/githubflow/",
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