How To Install snp-sites on Debian 9
Introduction
In this tutorial we learn how to install snp-sites on Debian 9.
What is snp-sites
snp-sites is:
This program finds single nucleotide polymorphism (SNP) sites from multi-fasta alignment input files (which might be compressed). Its output can be in various widely used formats (Multi Fasta Alignment, Vcf, phylip).
The software has been developed at the Wellcome Trust Sanger Institute.
A Single Nucleotide - polymorphism (SNP, pronounced snip; plural snips) is a DNA sequence variation occurring when a Single Nucleotide ?? A, T, C or G ?? in the genome (or other shared sequence) differs between members of a biological species or paired chromosomes. For example, two sequenced DNA fragments from different individuals, AAGCCTA to AAGCTTA, contain a difference in a single nucleotide. In this case there are two alleles. Almost all common SNPs have only two alleles.
There are three methods to install snp-sites on Debian 9. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install snp-sites Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install snp-sites using apt-get by running the following command:
sudo apt-get -y install snp-sites
Install snp-sites Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install snp-sites using apt by running the following command:
sudo apt -y install snp-sites
Install snp-sites 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 snp-sites using aptitude by running the following command:
sudo aptitude -y install snp-sites
How To Uninstall snp-sites on Debian 9
To uninstall only the snp-sites package we can use the following command:
sudo apt-get remove snp-sites
Uninstall snp-sites And Its Dependencies
To uninstall snp-sites and its dependencies that are no longer needed by Debian 9, we can use the command below:
sudo apt-get -y autoremove snp-sites
Remove snp-sites Configurations and Data
To remove snp-sites configuration and data from Debian 9 we can use the following command:
sudo apt-get -y purge snp-sites
Remove snp-sites configuration, data, and all of its dependencies
We can use the following command to remove snp-sites configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge snp-sites
Dependencies
snp-sites have the following dependencies:
References
Summary
In this tutorial we learn how to install snp-sites package on Debian 9 using different package management tools: apt, apt-get and aptitude.