How To Install gmap on Ubuntu 22.04
Introduction
In this tutorial we learn how to install gmap on Ubuntu 22.04.
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 Ubuntu 22.04. 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 first since aptitude is usually not installed by default on Ubuntu. 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 Ubuntu 22.04
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 Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove gmap
Remove gmap Configurations and Data
To remove gmap configuration and data from Ubuntu 22.04 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
References
Summary
In this tutorial we learn how to install gmap package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.
