How To Install pirs-examples on Ubuntu 18.04
Introduction
In this tutorial we learn how to install pirs-examples on Ubuntu 18.04.
What is pirs-examples
pirs-examples 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.
This package contains some example data.
There are three methods to install pirs-examples on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install pirs-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 pirs-examples using apt-get by running the following command:
sudo apt-get -y install pirs-examples
Install pirs-examples Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install pirs-examples using apt by running the following command:
sudo apt -y install pirs-examples
Install pirs-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 Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install pirs-examples using aptitude by running the following command:
sudo aptitude -y install pirs-examples
How To Uninstall pirs-examples on Ubuntu 18.04
To uninstall only the pirs-examples package we can use the following command:
sudo apt-get remove pirs-examples
Uninstall pirs-examples And Its Dependencies
To uninstall pirs-examples and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove pirs-examples
Remove pirs-examples Configurations and Data
To remove pirs-examples configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge pirs-examples
Remove pirs-examples configuration, data, and all of its dependencies
We can use the following command to remove pirs-examples configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge pirs-examples
References
Summary
In this tutorial we learn how to install pirs-examples package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
