How To Install perm on Kali Linux

In this tutorial we learn how to install perm on Kali Linux. perm is efficient mapping of short reads with periodic spaced seeds

Introduction

In this tutorial we learn how to install perm on Kali Linux.

What is perm

perm is:

PerM is a software package which was designed to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. Today PerM is capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.

There are three methods to install perm 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 perm Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install perm

Install perm Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install perm using apt by running the following command:

sudo apt -y install perm

Install perm 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 perm using aptitude by running the following command:

sudo aptitude -y install perm

How To Uninstall perm on Kali Linux

To uninstall only the perm package we can use the following command:

sudo apt-get remove perm

Uninstall perm And Its Dependencies

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

sudo apt-get -y autoremove perm

Remove perm Configurations and Data

To remove perm configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge perm

Remove perm configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge perm

Dependencies

perm have the following dependencies:

References

Summary

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