Python and the Surrounding Software Ecology

We will start by installing the basic software that is required for most of this book. This will include the Python distribution, some fundamental Python libraries, and external bioinformatics software. Here, we will also look at the world outside of Python. In bioinformatics and big data, R is also a major player; therefore, you will learn how to interact with it via rpy2, which is a Python/R bridge. Additionally, we will explore the advantages that the IPython framework (via Jupyter Lab) can give us in order to efficiently interface with R. Given that source management with Git and GitHub is pervasive, we will make sure that our setup plays well with them. This chapter will set the stage for all of the computational biologies that we will perform in the remainder of this book.

As different users have different requirements, we will cover two different approaches for installing the software. One approach is using the Anaconda Python ...