How To Install ggd-utils on Kali Linux
Introduction
In this tutorial we learn how to install ggd-utils on Kali Linux.
What is ggd-utils
ggd-utils is:
Takes a genome file and (currently) a .vcf.gz or a .bed.gz and checks that:
* a .tbi is present
* the VCF has ""##fileformat=VCF" as the first
line
* the VCF has a #CHROM header
* the chromosome are in the order specified by
the genome file (and present)
* the positions are sorted
* the positions are <= the chromosome lengths
defined in the genome file.
As a result, any new genome going into GGD will have a .genome file that will dictate the sort order and presence or absence of the ‘chr’ prefix for chromosomes
There are three methods to install ggd-utils on Kali Linux. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install ggd-utils Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get updateAfter updating apt database, We can install ggd-utils using apt-get by running the following command:
sudo apt-get -y install ggd-utilsInstall ggd-utils Using apt
Update apt database with apt using the following command.
sudo apt updateAfter updating apt database, We can install ggd-utils using apt by running the following command:
sudo apt -y install ggd-utilsInstall ggd-utils Using aptitude
If you want to follow this method, you might need to install aptitude on Kali Linux first since aptitude is usually not installed by default on Kali Linux. Update apt database with aptitude using the following command.
sudo aptitude updateAfter updating apt database, We can install ggd-utils using aptitude by running the following command:
sudo aptitude -y install ggd-utilsHow To Uninstall ggd-utils on Kali Linux
To uninstall only the ggd-utils package we can use the following command:
sudo apt-get remove ggd-utilsUninstall ggd-utils And Its Dependencies
To uninstall ggd-utils and its dependencies that are no longer needed by Kali Linux, we can use the command below:
sudo apt-get -y autoremove ggd-utilsRemove ggd-utils Configurations and Data
To remove ggd-utils configuration and data from Kali Linux we can use the following command:
sudo apt-get -y purge ggd-utilsRemove ggd-utils configuration, data, and all of its dependencies
We can use the following command to remove ggd-utils configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge ggd-utilsDependencies
ggd-utils have the following dependencies:
References
Summary
In this tutorial we learn how to install ggd-utils package on Kali Linux using different package management tools: apt, apt-get and aptitude.
