How To Install mindthegap-examples on Debian 12
Introduction
In this tutorial we learn how to install mindthegap-examples on Debian 12.
What is mindthegap-examples
mindthegap-examples 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 gap between a set of input contigs without any a priori on their relative order and orientation. It outputs the results in gfa file. Please note that this package is meant to accommodate the mindthegap package and only acts as example to how this package can be utilised.
There are three methods to install mindthegap-examples on Debian 12. 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-examples 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-examples using apt-get by running the following command:
sudo apt-get -y install mindthegap-examples
Install mindthegap-examples Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install mindthegap-examples using apt by running the following command:
sudo apt -y install mindthegap-examples
Install mindthegap-examples 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 mindthegap-examples using aptitude by running the following command:
sudo aptitude -y install mindthegap-examples
How To Uninstall mindthegap-examples on Debian 12
To uninstall only the mindthegap-examples package we can use the following command:
sudo apt-get remove mindthegap-examples
Uninstall mindthegap-examples And Its Dependencies
To uninstall mindthegap-examples and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove mindthegap-examples
Remove mindthegap-examples Configurations and Data
To remove mindthegap-examples configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge mindthegap-examples
Remove mindthegap-examples configuration, data, and all of its dependencies
We can use the following command to remove mindthegap-examples configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge mindthegap-examples
Dependencies
mindthegap-examples have the following dependencies:
References
Summary
In this tutorial we learn how to install mindthegap-examples package on Debian 12 using different package management tools: apt, apt-get and aptitude.
