How To Install ska on Debian 12
Introduction
In this tutorial we learn how to install ska on Debian 12.
What is ska
ska is:
SKA (Split Kmer Analysis) is a toolkit for prokaryotic (and any other small, haploid) DNA sequence analysis using split kmers. A split kmer is a pair of kmers in a DNA sequence that are separated by a single base. Split kmers allow rapid comparison and alignment of small genomes, and is particulalry suited for surveillance or outbreak investigation. SKA can produce split kmer files from fasta format assemblies or directly from fastq format read sequences, cluster them, align them with or without a reference sequence and provide various comparison and summary statistics. Currently all testing has been carried out on high-quality Illumina read data, so results for other platforms may vary.
There are three methods to install ska on Debian 12. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install ska Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install ska using apt-get by running the following command:
sudo apt-get -y install ska
Install ska Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install ska using apt by running the following command:
sudo apt -y install ska
Install ska 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 Debian. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install ska using aptitude by running the following command:
sudo aptitude -y install ska
How To Uninstall ska on Debian 12
To uninstall only the ska package we can use the following command:
sudo apt-get remove ska
Uninstall ska And Its Dependencies
To uninstall ska and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove ska
Remove ska Configurations and Data
To remove ska configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge ska
Remove ska configuration, data, and all of its dependencies
We can use the following command to remove ska configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge ska
Dependencies
ska have the following dependencies:
References
Summary
In this tutorial we learn how to install ska package on Debian 12 using different package management tools: apt, apt-get and aptitude.