How To Install smrtanalysis on Ubuntu 18.04
Introduction
In this tutorial we learn how to install smrtanalysis on Ubuntu 18.04.
What is smrtanalysis
smrtanalysis is:
SMRT® Analysis is a powerful, open-source bioinformatics software suite available for analysis of DNA sequencing data from Pacific Biosciences’ SMRT technology. Users can choose from a variety of analysis protocols that utilize PacBio® and third-party tools. Analysis protocols include de novo genome assembly, cDNA mapping, DNA base-modification detection, and long-amplicon analysis to determine phased consensus sequences.
This is a metapackage that depends on the components of SMRT Analysis.
There are three methods to install smrtanalysis 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 smrtanalysis Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install smrtanalysis using apt-get by running the following command:
sudo apt-get -y install smrtanalysis
Install smrtanalysis Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install smrtanalysis using apt by running the following command:
sudo apt -y install smrtanalysis
Install smrtanalysis 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 smrtanalysis using aptitude by running the following command:
sudo aptitude -y install smrtanalysis
How To Uninstall smrtanalysis on Ubuntu 18.04
To uninstall only the smrtanalysis package we can use the following command:
sudo apt-get remove smrtanalysis
Uninstall smrtanalysis And Its Dependencies
To uninstall smrtanalysis and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove smrtanalysis
Remove smrtanalysis Configurations and Data
To remove smrtanalysis configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge smrtanalysis
Remove smrtanalysis configuration, data, and all of its dependencies
We can use the following command to remove smrtanalysis configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge smrtanalysis
References
Summary
In this tutorial we learn how to install smrtanalysis package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
