How To Install seer on Ubuntu 18.04
Introduction
In this tutorial we learn how to install seer on Ubuntu 18.04.
What is seer
seer is:
Bacterial genomes vary extensively in terms of both gene content and gene sequence - this plasticity hampers the use of traditional SNP-based methods for identifying all genetic associations with phenotypic variation. SEER provides a computationally scalable and widely applicable statistical method for the identification of sequence elements that are significantly enriched in a phenotype of interest. SEER is applicable to even tens of thousands of genomes by counting variable- length k-mers using a distributed string-mining algorithm. Robust options are provided for association analysis that also correct for the clonal population structure of bacteria. Using large collections of genomes of the major human pathogen Streptococcus pneumoniae, SEER identifies relevant previously characterised resistance determinants for several antibiotics.
There are three methods to install seer 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 seer Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install seer using apt-get by running the following command:
sudo apt-get -y install seer
Install seer Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install seer using apt by running the following command:
sudo apt -y install seer
Install seer 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 seer using aptitude by running the following command:
sudo aptitude -y install seer
How To Uninstall seer on Ubuntu 18.04
To uninstall only the seer package we can use the following command:
sudo apt-get remove seer
Uninstall seer And Its Dependencies
To uninstall seer and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove seer
Remove seer Configurations and Data
To remove seer configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge seer
Remove seer configuration, data, and all of its dependencies
We can use the following command to remove seer configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge seer
References
Summary
In this tutorial we learn how to install seer package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
