How To Install pirs on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 458 words
Introduction
In this tutorial we learn how to install pirs on Ubuntu.
What is pirs
pirs is:
The program pIRS can be used for simulating Illumina PE reads, with a series of characters generated by Illumina sequencing platform, such as insert size distribution, sequencing error(substitution, insertion, deletion), quality score and GC content-coverage bias.
The insert size follows a normal distribution, so users should set the mean value and standard deviation. Usually the standard deviation is set as 1/20 of the mean value. The normal distribution by Box-Muller method is simulated.
The program simulates sequencing error, quality score and GC content- coverage bias according to the empirical distribution profile. Some default profiles counted from lots of real sequencing data are provided.
To simulate reads from diploid genome, users should simulate the diploid genome sequence firstly by setting the ratio of heterozygosis SNP, heterozygosis InDel and structure variation.
There are three methods to install pirs on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install pirs Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install pirs using apt-get by running the following command:
sudo apt-get -y install pirs
Install pirs Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install pirs using apt by running the following command:
sudo apt -y install pirs
Install pirs 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 pirs using aptitude by running the following command:
sudo aptitude -y install pirs
How To Uninstall pirs on Ubuntu
To uninstall only the pirs package we can use the following command:
sudo apt-get remove pirs
Uninstall pirs And Its Dependencies
To uninstall pirs and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove pirs
Remove pirs Configurations and Data
To remove pirs configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge pirs
Remove pirs configuration, data, and all of its dependencies
We can use the following command to remove pirs configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge pirs
Dependencies
pirs have the following dependencies:
References
Summary
In this tutorial we learn how to install pirs package on Ubuntu using different package management tools: apt, apt-get and aptitude.