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
- [ ] re-implement the archive/encryption interface [@ingkebil]
- [ ] handle clean up of expired bundles [@robinandeer]
- [ ] expand the CLI with get command etc. [@robinandeer]
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 . `
Housekeeper is using github flow branching model as described in our [development manual][development manual].
### 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/ [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/
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