How To Install python3-pairtools on Ubuntu 22.04
Introduction
In this tutorial we learn how to install python3-pairtools
on Ubuntu 22.04.
What is python3-pairtools
python3-pairtools is:
Simple and fast command-line framework to process sequencing data from a Hi-C experiment.
Process pair-end sequence alignments and perform the following operations:
- Detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end sequences of Hi-C DNA molecules
- Sort .pairs files for downstream analyses
- Detect, tag and remove PCR/optical duplicates
- Generate extensive statistics of Hi-C datasets
- Select Hi-C pairs given flexibly defined criteria
- Restore .sam alignments from Hi-C pairs
There are three methods to install python3-pairtools
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 python3-pairtools Using apt-get
Update apt database with apt-get
using the following command.
sudo apt-get update
After updating apt database, We can install python3-pairtools
using apt-get
by running the following command:
sudo apt-get -y install python3-pairtools
Install python3-pairtools Using apt
Update apt database with apt
using the following command.
sudo apt update
After updating apt database, We can install python3-pairtools
using apt
by running the following command:
sudo apt -y install python3-pairtools
Install python3-pairtools 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 python3-pairtools
using aptitude
by running the following command:
sudo aptitude -y install python3-pairtools
How To Uninstall python3-pairtools on Ubuntu 22.04
To uninstall only the python3-pairtools
package we can use the following command:
sudo apt-get remove python3-pairtools
Uninstall python3-pairtools And Its Dependencies
To uninstall python3-pairtools
and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove python3-pairtools
Remove python3-pairtools Configurations and Data
To remove python3-pairtools
configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge python3-pairtools
Remove python3-pairtools configuration, data, and all of its dependencies
We can use the following command to remove python3-pairtools
configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge python3-pairtools
References
Summary
In this tutorial we learn how to install python3-pairtools
package on Ubuntu 22.04 using different package management tools: apt
, apt-get
and aptitude
.