How To Install tophat on Debian 10
Introduction
In this tutorial we learn how to install tophat on Debian 10.
What is tophat
tophat is:
TopHat aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. TopHat is a collaborative effort between the University of Maryland Center for Bioinformatics and Computational Biology and the University of California, Berkeley Departments of Mathematics and Molecular and Cell Biology.
There are three methods to install tophat on Debian 10. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install tophat Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install tophat using apt-get by running the following command:
sudo apt-get -y install tophat
Install tophat Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install tophat using apt by running the following command:
sudo apt -y install tophat
Install tophat 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 tophat using aptitude by running the following command:
sudo aptitude -y install tophat
How To Uninstall tophat on Debian 10
To uninstall only the tophat package we can use the following command:
sudo apt-get remove tophat
Uninstall tophat And Its Dependencies
To uninstall tophat and its dependencies that are no longer needed by Debian 10, we can use the command below:
sudo apt-get -y autoremove tophat
Remove tophat Configurations and Data
To remove tophat configuration and data from Debian 10 we can use the following command:
sudo apt-get -y purge tophat
Remove tophat configuration, data, and all of its dependencies
We can use the following command to remove tophat configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge tophat
Dependencies
tophat have the following dependencies:
References
Summary
In this tutorial we learn how to install tophat package on Debian 10 using different package management tools: apt, apt-get and aptitude.