StaPH-B ToolKit

A python library designed to make programs held within the StaPH-B Docker repository more accessible to public health scientists.

Summary

The StaPH-B ToolKit is a Python library of commonly used bioinformatics tools that help to inform public health action. The StaPH-B ToolKit utilizes the StaPH-B Docker Images to enable easy access of open-source software without the need of local installation and/or dependency maintenance.

Motivation

Public health bioinformatics is dependent on open-source software that require carefully curated computational environments and various software dependencies. Setting up and maintaining such environments requires a skill set and expertise absent in most public health laboratories. The StaPH-B Docker Images have helped generate reproducible computational environments through the use of containerization. However, access to these images is dependent on a working understanding of containerization, which is not available in most laboratories. The ToolKit addresses this issue through the handling of the StaPH-B docker images allowing users to interact with bioinformatis programs without needing to interact directly with mounted file systems and running containers. The goal of the Toolkit is it increase usability while mirroring the functionality of a locally-installed tool.

Installing and Usage

The ToolKit requires either singularity or docker, Python 3.6 or greater, and Java version 8 or later. The documentation for installing the dependencies can be found here: https://staph-b.github.io/staphb_toolkit.
The ToolKit itself can be installed using pip or git:

To install using pip:

$ pip install staphb_toolkit

To install using git:

$ git clone https://github.com/StaPH-B/staphb_toolkit.git
$ ./staphb_toolkit/setup.py

Test the pipeline with the following command and ensure you see the same usage output:

$ staphb-tk
usage: staphb-tk [optional arguments] <application> [application arguments]

optional arguments:
  -h, --help            show this help message and exit
  --docker_config <path>, -c <path>
                        Configuration file for container images and tags; if
                        none provided, default container versions will be
                        used.
  --get_docker_config   Get the default docker container configureation file.
  --list, -l            List all of the software available in the toolkit.
  --update              Check for and install a ToolKit update.
  --auto_update         Toggle automatic ToolKit updates. Default is off.

custom toolkit application:

    mash_species        MASH Species uses a custom database to identify the
                        isolate species.