housekeeper 4.13.9

File data orchestrator

Housekeeper

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

Installation

Housekeeper written in Python 3.6+ and is available on the Python Package Index (PyPI).

poetry install

If you would like to install the latest development version:

git clone https://github.com/Clinical-Genomics/housekeeper
cd housekeeper
poetry install

Contributing

Housekeeper is using GitHub flow branching model as described in our development manual.

Documentation

Command line interface

Config file

Housekeeper supports a basic YAML config. The following options are supported:

---
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.

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.

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.