How To Install gmap on Kali Linux

Introduction

In this tutorial we learn how to install gmap on Kali Linux.

What is gmap

gmap is:

This package contains the programs GMAP and GSNAP as well as utilities to manage genome databases in GMAP/GSNAP format. GMAP (Genomic Mapping and Alignment Program) is a tool for aligning EST, mRNA and cDNA sequences. GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for aligning single-end and paired-end transcriptome reads. Both tools can use a database of

• known splice sites and identify novel splice sites.
• known single-nucleotide polymorphisms (SNPs). GSNAP can align bisulfite-treated DNA.

There are three methods to install gmap 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 gmap Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install gmap using apt-get by running the following command:

sudo apt-get -y install gmap

Install gmap Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install gmap using apt by running the following command:

sudo apt -y install gmap

Install gmap 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 update

After updating apt database, We can install gmap using aptitude by running the following command:

sudo aptitude -y install gmap

How To Uninstall gmap on Kali Linux

To uninstall only the gmap package we can use the following command:

sudo apt-get remove gmap

Uninstall gmap And Its Dependencies

To uninstall gmap and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove gmap

Remove gmap Configurations and Data

To remove gmap configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge gmap

Remove gmap configuration, data, and all of its dependencies

We can use the following command to remove gmap configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge gmap

Dependencies

gmap have the following dependencies:

• perl

References

• gmap website

Summary

In this tutorial we learn how to install gmap package on Kali Linux using different package management tools: apt, apt-get and aptitude.