How To Install idseq-bench on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
2 minutes • 381 words
Introduction
In this tutorial we learn how to install idseq-bench on Ubuntu.
What is idseq-bench
idseq-bench is:
IDseq (Infectious Disease Sequencing Platform) is an unbiased global software platform that helps scientists identify pathogens in metagenomic sequencing data.
- Discover - Identify the pathogen landscape
- Detect - Monitor and review potential outbreaks
- Decipher - Find potential infecting organisms in large datasets
This package provides the benchmark generator for the IDseq Portal.
There are three methods to install idseq-bench 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 idseq-bench Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install idseq-bench using apt-get by running the following command:
sudo apt-get -y install idseq-bench
Install idseq-bench Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install idseq-bench using apt by running the following command:
sudo apt -y install idseq-bench
Install idseq-bench 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 idseq-bench using aptitude by running the following command:
sudo aptitude -y install idseq-bench
How To Uninstall idseq-bench on Ubuntu
To uninstall only the idseq-bench package we can use the following command:
sudo apt-get remove idseq-bench
Uninstall idseq-bench And Its Dependencies
To uninstall idseq-bench and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove idseq-bench
Remove idseq-bench Configurations and Data
To remove idseq-bench configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge idseq-bench
Remove idseq-bench configuration, data, and all of its dependencies
We can use the following command to remove idseq-bench configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge idseq-bench
Dependencies
idseq-bench have the following dependencies:
References
Summary
In this tutorial we learn how to install idseq-bench package on Ubuntu using different package management tools: apt, apt-get and aptitude.