How To Install sspace on Ubuntu 18.04
Introduction
In this tutorial we learn how to install sspace on Ubuntu 18.04.
What is sspace
sspace is:
SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension (SSPACE) is a script able to extend and scaffold pre-assembled contigs using one or more mate pairs or paired-end libraries, or even a combination.
SSPACE is built based on SSAKE. Code of SSAKE is changed to be able to extend and scaffold pre-assembled contigs for multiple paired reads libraries.
This is the free ‘basic’ version of SSPACE. The non-free ‘standard’ version is available directly from Baseclear.
There are three methods to install sspace 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 sspace Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install sspace using apt-get by running the following command:
sudo apt-get -y install sspace
Install sspace Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install sspace using apt by running the following command:
sudo apt -y install sspace
Install sspace 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 sspace using aptitude by running the following command:
sudo aptitude -y install sspace
How To Uninstall sspace on Ubuntu 18.04
To uninstall only the sspace package we can use the following command:
sudo apt-get remove sspace
Uninstall sspace And Its Dependencies
To uninstall sspace and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove sspace
Remove sspace Configurations and Data
To remove sspace configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge sspace
Remove sspace configuration, data, and all of its dependencies
We can use the following command to remove sspace configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge sspace
References
Summary
In this tutorial we learn how to install sspace package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
