3  Package managers

3.1 What is the importance of package managers

3.2 Conda environments

What is conda:

To install conda (the command), miniconda (the lighter distribution).

For Linux x86_64 machine

curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

For Mac (Intel, will also works on M1):

curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh

Once downloaded, the next step is to run the installation script.

bash Miniconda3-latest-Linux-x86_64.sh

After installation is completed, it is recommended to add the following channels to your conda configuration. Conda channels are…

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

After this, conda should be installed, you may need to restart your terminal.

Tip

A faster implementation of the conda command is mamba. To install it simply run conda install mamba and then every time you will install a program just substitute conda for mamba

3.3 Package managers for OS

There are several package managers handling general purpose packages and apps. For MacOS the famous one is Homebrew and for Windows several could be used such as Chocolatey and Scoop.