How To Install snpomatic on Ubuntu 18.04
Introduction
In this tutorial we learn how to install snpomatic on Ubuntu 18.04.
What is snpomatic
snpomatic is:
High throughput sequencing technologies generate large amounts of short reads. Mapping these to a reference sequence consumes large amounts of processing time and memory, and read mapping errors can lead to noisy or incorrect alignments.
SNP-o-matic is a fast, stringent short-read mapping software. It supports a multitude of output types and formats, for uses in filtering reads, alignments, sequence-based genotyping calls, assisted reassembly of contigs etc.
There are three methods to install snpomatic 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 snpomatic Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install snpomatic using apt-get by running the following command:
sudo apt-get -y install snpomatic
Install snpomatic Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install snpomatic using apt by running the following command:
sudo apt -y install snpomatic
Install snpomatic 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 snpomatic using aptitude by running the following command:
sudo aptitude -y install snpomatic
How To Uninstall snpomatic on Ubuntu 18.04
To uninstall only the snpomatic package we can use the following command:
sudo apt-get remove snpomatic
Uninstall snpomatic And Its Dependencies
To uninstall snpomatic and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove snpomatic
Remove snpomatic Configurations and Data
To remove snpomatic configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge snpomatic
Remove snpomatic configuration, data, and all of its dependencies
We can use the following command to remove snpomatic configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge snpomatic
References
Summary
In this tutorial we learn how to install snpomatic package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
