How To Install discosnp on Debian 9
Introduction
In this tutorial we learn how to install discosnp on Debian 9.
What is discosnp
discosnp is:
Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).
Note that number of input read sets is not constrained, it can be one, two, or more. Note also that no other data as reference genome or annotations are needed.
The software is composed by two modules. First module, kissnp2, detects SNPs from read sets. A second module, kissreads, enhance the kissnp2 results by computing per read set and for each found SNP:
- its mean read coverage
- the (phred) quality of reads generating the polymorphism.
There are three methods to install discosnp 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 discosnp Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install discosnp using apt-get by running the following command:
sudo apt-get -y install discosnp
Install discosnp Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install discosnp using apt by running the following command:
sudo apt -y install discosnp
Install discosnp 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 discosnp using aptitude by running the following command:
sudo aptitude -y install discosnp
How To Uninstall discosnp on Debian 9
To uninstall only the discosnp package we can use the following command:
sudo apt-get remove discosnp
Uninstall discosnp And Its Dependencies
To uninstall discosnp and its dependencies that are no longer needed by Debian 9, we can use the command below:
sudo apt-get -y autoremove discosnp
Remove discosnp Configurations and Data
To remove discosnp configuration and data from Debian 9 we can use the following command:
sudo apt-get -y purge discosnp
Remove discosnp configuration, data, and all of its dependencies
We can use the following command to remove discosnp configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge discosnp
Dependencies
discosnp have the following dependencies:
References
Summary
In this tutorial we learn how to install discosnp package on Debian 9 using different package management tools: apt, apt-get and aptitude.