Technical requirements

The code for this chapter can be found at https://github.com/PacktPublishing/Bioinformatics-with-Python-Cookbook-Fourth-Edition/tree/main/Ch15.

You will want to create a Ch15 folder and set up your notebooks there. In this chapter, we will work within three sub-folders for the respective tools we’ll be learning about: Galaxy, Snakemake, and Nextflow.

Remember to activate your conda environment before beginning the recipes, like this:

conda activate bioinformatics_base

Or, if you would like to set up a conda environment specific to this chapter, before activating bioinformatics_base, run the following:

conda create -n ch15-workflows --clone bioinformatics_base
conda activate ch15-workflows

You will be able to install the packages for the chapter as you go, or you can use the YAML file provided in the repository:

conda env update --file ch15-workflows.yml