The Toolkit uses containerized applications that package the dependencies of each tool in a single “container”. The ToolKit also provides access to workflows developed using Nextflow. The ToolKit was developed using Python 3.7 which can easily be installed on any Unix/Linux operating system following the instructions below. The design philosophy is centered around usability including the installation of dependencies. Using containerization and Nextflow the Toolkit is able has access to a variety of bioinformatics applications and pipelines with out the necessity of installing various often conflicting dependencies. However, because of the use of containerization and Nextflow there are several dependencies that are unavoidable.

Python

The Toolkit uses python version >= 3.7 to interact with the containers and workflows. Most Linux systems come with an adequate version of python.
To check your version of python use the following command:

python -V

If you do not have Python 3.7 or greater the best way to install python is using the package installer Anaconda. This can be done on an Debian/Ubuntu Linux system with the following commands (Installs Python 3.9):

sudo apt-get install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 libxcomposite1 libasound2 libxi6 libxtst6
wget https://repo.anaconda.com/archive/Anaconda3-2022.05-Linux-x86_64.sh
bash Anaconda3-2022.05-Linux-x86_64.sh
source ~/.bashrc

Note: When prompted with “Do you wish the installer to initialize Anaconda3 by running conda init?” We recommend “yes”.

For a different system download it through the Anaconda Install and follow the instructions here: Anaconda Install.

Docker or Singularity

The system must have either Docker or Singularity installed in order to use any of the tools in the Toolkit.

Docker

To check if you have docker installed and working use the following command:

docker --version
docker run hello-world

Installation instructions for installing Docker on an Ubuntu Linux system:

sudo apt-get update
sudo apt install apt-transport-https ca-certificates curl gnupg-agent software-properties-common
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable"
sudo apt-get update
sudo apt-get install docker-ce docker-ce-cli containerd.io
sudo usermod -aG docker ${USER}
sudo su - ${USER}

Singularity

To check if you have singularity installed and working use the following command:

singularity --version
singularity run library://sylabsed/examples/lolcow

Installation instructions for installing Singularity on an Debian/Ubuntu Linux system:

sudo wget -O- http://neuro.debian.net/lists/xenial.us-ca.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
sudo apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9
sudo apt-get update
sudo apt-get install singularity-container

Java

The ToolKit needs Java version 8 or later, check your java version using:

java -version

Install version 8 using the following command or replace the 8 with a newer version if you wish, i.e. openjdk-12-jre.

sudo apt-get install openjdk-8-jre

Installing the ToolKit

To install using pip:

$ pip install staphb_toolkit

To install using git: