Installing the required basic software with Anaconda

Before we get started, we need to install some basic prerequisite software. The following sections will take you through the software and the steps that are needed to install them. Each chapter and section might have extra requirements on top of these – we will make those clear as the book progresses. An alternative way to start is to use the Docker recipe, after which everything will be taken care of for you via a Docker container.

If you are already using a different Python distribution, you are strongly encouraged to consider Anaconda, as it has become the de-facto standard for data science and bioinformatics. Also, it is the distribution that will allow you to install software from Bioconda (https://bioconda.github.io/).

Getting ready

Python can be run on top of different environments. For instance, you can use Python inside the Java Virtual Machine (JVM) (via Jython or with .NET via IronPython). However, here...