Package Managers Conda and Mamba
This is a primer for the use of package managers Conda and the related Mamba. This is not essential for following the tutorial but is nevertheless useful when working with command-line and bioinformatics.
If you are already familiar with package managers, don’t want to waste more time or already had enough IT concepts to learn and are keen to start with the tutorials feel free to moce on to Long-Read data analysis workflow
An Introduction to Package Managers
Installing new apps/softwares and all the things required, the dependencies, on a GUI such as Windows requires only a double-click on the installer program.
On the command-line, it usually requires several commands to install a new tool and, in contrast GUI installers, often the dependencies for a tools will have to be manually installed before the installation of the tool that needs them. To further complicate the installation on the command-line, the dependencies of some tools may conflict with other tools. For example, if tool A requires the programming language Python version 2.2 but another program, tool B, requires Python version 3.3 as dependencies then the user will first find a solution for the conflicting dependencies before tools A and B can both be installed on the system.
Package Managers are collections of scripts and programs that helps users to decomplicate the installation of tools on the command-line and manage their dependencies. Most linux distributions come with their own package managers installed, e.g. aptitude for Ubuntu and zypper for Suse. A very popular cross-platform pacakge manager, i.e., it can be used on most/all computer “platforms”, is the package manager Conda. Conda provides not only a user-friendly way of installing tools and packages including it’s dependencies but creates so called environments in which the packages are installed into minimising the potential for conflicts between packages.