Metadata-Version: 2.1
Name: housekeeper
Version: 3.0.1
Summary: Housekeeper takes care of files
Home-page: https://github.com/Clinical-Genomics/housekeeper
Author: Robin Andeer
Author-email: mans.magnusson@scilifelab.se
License: MIT
Description: 
        # Housekeeper
        ![Housekeeper tests][github-url] [![Coverage Status][coveralls-image]][coveralls-url] [![CodeFactor][codefactor-image]][codefactor-url] [![Code style: black][black-image]][black-url]
        
        ### Store, tag, fetch, and archive files with ease 🗃
        
        **Housekeeper** is a tool that aims to provide:
        
        - a backend for storing versioned bundles of files
        - different interfaces (Python, CLI, REST) for fetching files based on tags
        - a way to backup and retrieve bundles from long-term storage
        
        ### Todo
        
        - [ ] re-implement the archive/encryption interface [@ingkebil]
        - [ ] handle clean up of expired bundles [@robinandeer]
        - [ ] expand the CLI with `get` command etc. [@robinandeer]
        
        ## Installation
        
        Housekeeper written in Python 3.6+ and is available on the [Python Package Index][pypi] (PyPI).
        
        ```bash
        pip install housekeeper
        ```
        
        If you would like to install the latest development version:
        
        ```bash
        git clone https://github.com/Clinical-Genomics/housekeeper
        cd housekeeper
        pip install --editable .
        ```
        
        ## Contributing
        
        Housekeeper is using github flow branching model as described in our [development manual][development manual].
        
        ## Documentation
        
        ### Command line interface
        
        #### Config file
        
        Housekeeper supports a very simple YAML config. The following options are supported:
        
        ```yaml
        ---
        database: mysql+pymysql://userName:passWord@domain.com/database
        root: /path/to/root/dir
        ```
        
        The `root` option is used to store files within the Housekeeper context.
        
        #### Command: `init`
        
        Setup (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.
        
        ```bash
        housekeeper --database "sqlite:///hk.sqlite3" init
        Success! New tables: bundle, file, file_tag_link, tag, version
        ```
        
        #### Command: `include`
        
        Include (hard-link) all files of an existing bundle version into Housekeeper and the `root` path.
        
        ```bash
        housekeeper myBundle
        ```
        
        This 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.
        
        #### Command: `delete files`
        
        Delete files that are not on disk anymore like his:
        `housekeeper delete files --tag fastq --notondisk`
        
        Remove all bam files before a certain date:
        `housekeeper delete files --tag bam --before 2017-06-15`
        
        Remove fastq files from a flowcell:
        `housekeeper delete files --tag fastq --tag H0HKKALXX`
        
        It'll always ask for confirmation, unless you add --yes:
        `housekeeper delete files --bundle sillyfish --yes`
        
        If you do not provide a --tag or --bundle, essentially deleting everything, the function will not let you do that.
        
        [pypi]: https://pypi.python.org/pypi/housekeeper/
        [coveralls-url]: https://coveralls.io/r/Clinical-Genomics/housekeeper
        [coveralls-image]: https://img.shields.io/coveralls/Clinical-Genomics/housekeeper.svg?style=flat-square
        [github-url]: https://github.com/Clinical-Genomics/housekeeper/workflows/Housekeeper%20tests/badge.svg
        [development manual]: http://www.clinicalgenomics.se/development/dev/githubflow/
        [codefactor-image]: https://www.codefactor.io/repository/github/clinical-genomics/housekeeper/badge
        [codefactor-url]: https://www.codefactor.io/repository/github/clinical-genomics/housekeeper
        [black-image]: https://img.shields.io/badge/code%20style-black-000000.svg
        [black-url]: https://github.com/psf/black
Keywords: housekeeper development
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Environment :: Console
Description-Content-Type: text/markdown
