How To Install snakemake on Ubuntu 18.04
Introduction
In this tutorial we learn how to install snakemake on Ubuntu 18.04.
What is snakemake
snakemake is:
Build systems like GNU Make are frequently used to create complicated workflows, e.g. in bioinformatics. This project aims to reduce the complexity of creating workflows by providing a clean and modern domain specific language (DSL) in Python style, together with a fast and comfortable execution environment.
There are three methods to install snakemake on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install snakemake Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install snakemake using apt-get by running the following command:
sudo apt-get -y install snakemake
Install snakemake Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install snakemake using apt by running the following command:
sudo apt -y install snakemake
Install snakemake Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install snakemake using aptitude by running the following command:
sudo aptitude -y install snakemake
How To Uninstall snakemake on Ubuntu 18.04
To uninstall only the snakemake package we can use the following command:
sudo apt-get remove snakemake
Uninstall snakemake And Its Dependencies
To uninstall snakemake and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove snakemake
Remove snakemake Configurations and Data
To remove snakemake configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge snakemake
Remove snakemake configuration, data, and all of its dependencies
We can use the following command to remove snakemake configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge snakemake
References
Summary
In this tutorial we learn how to install snakemake package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
