How To Install lumpy-sv on Kali Linux

In this tutorial we learn how to install lumpy-sv on Kali Linux. lumpy-sv is general probabilistic framework for structural variant discovery

Introduction

In this tutorial we learn how to install lumpy-sv on Kali Linux.

What is `lumpy-sv`

lumpy-sv is:

LUMPY, a novel SV discovery framework that naturally integrates multiple SV signals jointly across multiple samples. LUMPY yields improved sensitivity, especially when SV signal is reduced owing to either low coverage data or low intra-sample variant allele frequency.

There are three methods to install lumpy-sv on Kali Linux. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install lumpy-sv Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install lumpy-sv using apt-get by running the following command:

sudo apt-get -y install lumpy-sv

Install lumpy-sv Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install lumpy-sv using apt by running the following command:

sudo apt -y install lumpy-sv

Install lumpy-sv Using aptitude

If you want to follow this method, you might need to install aptitude on Kali Linux first since aptitude is usually not installed by default on Kali Linux. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install lumpy-sv using aptitude by running the following command:

sudo aptitude -y install lumpy-sv

How To Uninstall lumpy-sv on Kali Linux

To uninstall only the lumpy-sv package we can use the following command:

sudo apt-get remove lumpy-sv

Uninstall lumpy-sv And Its Dependencies

To uninstall lumpy-sv and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove lumpy-sv

Remove lumpy-sv Configurations and Data

To remove lumpy-sv configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge lumpy-sv

Remove lumpy-sv configuration, data, and all of its dependencies

We can use the following command to remove lumpy-sv configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge lumpy-sv

Dependencies

lumpy-sv have the following dependencies:

References

lumpy-sv website

Summary

In this tutorial we learn how to install lumpy-sv package on Kali Linux using different package management tools: apt, apt-get and aptitude.