How To Install plasmidid on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
2 minutes • 418 words
Introduction
In this tutorial we learn how to install plasmidid on Ubuntu.
What is plasmidid
plasmidid is:
PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.
PlasmidID is a computational pipeline that maps Illumina reads over plasmid database sequences. The k-mer filtered, most covered sequences are clustered by identity to avoid redundancy and the longest are used as scaffold for plasmid reconstruction. Reads are assembled and annotated by automatic and specific annotation. All information generated from mapping, assembly, annotation and local alignment analyses is gathered and accurately represented in a circular image which allow user to determine plasmidic composition in any bacterial sample.
There are three methods to install plasmidid on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install plasmidid Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install plasmidid using apt-get by running the following command:
sudo apt-get -y install plasmidid
Install plasmidid Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install plasmidid using apt by running the following command:
sudo apt -y install plasmidid
Install plasmidid 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 plasmidid using aptitude by running the following command:
sudo aptitude -y install plasmidid
How To Uninstall plasmidid on Ubuntu
To uninstall only the plasmidid package we can use the following command:
sudo apt-get remove plasmidid
Uninstall plasmidid And Its Dependencies
To uninstall plasmidid and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove plasmidid
Remove plasmidid Configurations and Data
To remove plasmidid configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge plasmidid
Remove plasmidid configuration, data, and all of its dependencies
We can use the following command to remove plasmidid configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge plasmidid
Dependencies
plasmidid have the following dependencies:
References
Summary
In this tutorial we learn how to install plasmidid package on Ubuntu using different package management tools: apt, apt-get and aptitude.