How To Install gsort on Debian 11
Introduction
In this tutorial we learn how to install gsort on Debian 11.
What is gsort
gsort is:
gsort is a tool to sort genomic files according to a genomefile. For example, to sort VCF to have order: X, Y, 2, 1, 3, … and the header needs to be kept at the top.
As a more likely example, if a file nneds to be sorted to match GATK order (1 … X, Y, MT) which is not possible with any other sorting tool. With gsort one can simply place MT as the last chrom in the “.genome” file.
It will also be useful for getting files ready for use in bedtools.
There are three methods to install gsort on Debian 11. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install gsort Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install gsort using apt-get by running the following command:
sudo apt-get -y install gsort
Install gsort Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install gsort using apt by running the following command:
sudo apt -y install gsort
Install gsort 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 gsort using aptitude by running the following command:
sudo aptitude -y install gsort
How To Uninstall gsort on Debian 11
To uninstall only the gsort package we can use the following command:
sudo apt-get remove gsort
Uninstall gsort And Its Dependencies
To uninstall gsort and its dependencies that are no longer needed by Debian 11, we can use the command below:
sudo apt-get -y autoremove gsort
Remove gsort Configurations and Data
To remove gsort configuration and data from Debian 11 we can use the following command:
sudo apt-get -y purge gsort
Remove gsort configuration, data, and all of its dependencies
We can use the following command to remove gsort configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge gsort
Dependencies
gsort have the following dependencies:
References
Summary
In this tutorial we learn how to install gsort package on Debian 11 using different package management tools: apt, apt-get and aptitude.