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stoker: exploration/curation of NGS data

Utility to help with managing copies of directories containing NGS data and analyses, developed within the Bioinformatics Core Facility (BCF) at the University of Manchester (UoM).

Overview

stoker provides a single utility of the same name, which has a number of subcommands:

  • compare: compares one directory against another, looking for missing, and extra file system 'objects' (files, directories and symbolic links), and objects which differ.
  • check_access: checks the accessibility of a directory for the current user and identifies objects which are not accessible due to file system permissions
  • find: reports objects matching specified criteria (e.g. file extensions)

Installation

It is recommended to use:

pip install .

from within the top-level source directory to install the package.

To use the package without installing it first you will need to add the directory to your PYTHONPATH environment.

To install directly from github using pip:

pip install git+https://github.com/pjbriggs/stoker.git

Documentation

This README currently comprises the whole of the documentation.

Authors

  • Peter Briggs (@pjbriggs)