How To Install cufflinks on Ubuntu 22.04
Introduction
In this tutorial we learn how to install cufflinks
on Ubuntu 22.04.
What is cufflinks
cufflinks is:
Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.
This package provides the binary of cufflinks and associated tools, i.e. compress_gtf, cuffcompare, cuffdiff, cuffmerge, cuffnorm, cuffquant and gtf_to_sam.
There are three methods to install cufflinks
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 cufflinks Using apt-get
Update apt database with apt-get
using the following command.
sudo apt-get update
After updating apt database, We can install cufflinks
using apt-get
by running the following command:
sudo apt-get -y install cufflinks
Install cufflinks Using apt
Update apt database with apt
using the following command.
sudo apt update
After updating apt database, We can install cufflinks
using apt
by running the following command:
sudo apt -y install cufflinks
Install cufflinks 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 cufflinks
using aptitude
by running the following command:
sudo aptitude -y install cufflinks
How To Uninstall cufflinks on Ubuntu 22.04
To uninstall only the cufflinks
package we can use the following command:
sudo apt-get remove cufflinks
Uninstall cufflinks And Its Dependencies
To uninstall cufflinks
and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove cufflinks
Remove cufflinks Configurations and Data
To remove cufflinks
configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge cufflinks
Remove cufflinks configuration, data, and all of its dependencies
We can use the following command to remove cufflinks
configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge cufflinks
References
Summary
In this tutorial we learn how to install cufflinks
package on Ubuntu 22.04 using different package management tools: apt
, apt-get
and aptitude
.