housekeeper 2.5.0

Housekeeper takes care of files.

# Housekeeper [![Build Status][travis-image]][travis-url] [![Coverage Status][coveralls-image]][coveralls-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:[e-mail]/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/ [travis-url]: https://travis-ci.org/Clinical-Genomics/housekeeper [travis-image]: https://img.shields.io/travis/Clinical-Genomics/housekeeper.svg?style=flat-square [coveralls-url]: https://coveralls.io/r/Clinical-Genomics/housekeeper [coveralls-image]: https://img.shields.io/coveralls/Clinical-Genomics/housekeeper.svg?style=flat-square [development manual]: http://www.clinicalgenomics.se/development/dev/githubflow/