How To Install mindthegap on Ubuntu 22.04
Introduction
In this tutorial we learn how to install mindthegap on Ubuntu 22.04.
What is mindthegap
mindthegap is:
Designed to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. It takes as input a set of reads and a reference genome. It outputs two sets of FASTA sequences: one is the set of breakpoints of detection insertion sites, the other is the set of assembled insertions for each breakpoint. MindTheGap can also be used as a genome assembly finishing tool. It can fill the gaps between a set of input contigs without any a priori on their relative order and orientation. It outputs the results in gfa file.
There are three methods to install mindthegap 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 mindthegap Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install mindthegap using apt-get by running the following command:
sudo apt-get -y install mindthegap
Install mindthegap Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install mindthegap using apt by running the following command:
sudo apt -y install mindthegap
Install mindthegap 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 mindthegap using aptitude by running the following command:
sudo aptitude -y install mindthegap
How To Uninstall mindthegap on Ubuntu 22.04
To uninstall only the mindthegap package we can use the following command:
sudo apt-get remove mindthegap
Uninstall mindthegap And Its Dependencies
To uninstall mindthegap and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove mindthegap
Remove mindthegap Configurations and Data
To remove mindthegap configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge mindthegap
Remove mindthegap configuration, data, and all of its dependencies
We can use the following command to remove mindthegap configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge mindthegap
References
Summary
In this tutorial we learn how to install mindthegap package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.
