How To Install paleomix on Ubuntu 22.04
Introduction
In this tutorial we learn how to install paleomix on Ubuntu 22.04.
What is paleomix
paleomix is:
The PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data: The BAM pipeline processes de-multiplexed reads from one or more samples, through sequence processing and alignment, to generate BAM alignment files useful in downstream analyses; the Phylogenetic pipeline carries out genotyping and phylogenetic inference on BAM alignment files, either produced using the BAM pipeline or generated elsewhere; and the Zonkey pipeline carries out a suite of analyses on low coverage equine alignments, in order to detect the presence of F1-hybrids in archaeological assemblages. In addition, PALEOMIX aids in metagenomic analysis of the extracts.
The pipelines have been designed with ancient DNA (aDNA) in mind, and includes several features especially useful for the analyses of ancient samples, but can all be for the processing of modern samples, in order to ensure consistent data processing.
There are three methods to install paleomix on Ubuntu 22.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install paleomix Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install paleomix using apt-get by running the following command:
sudo apt-get -y install paleomix
Install paleomix Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install paleomix using apt by running the following command:
sudo apt -y install paleomix
Install paleomix 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 paleomix using aptitude by running the following command:
sudo aptitude -y install paleomix
How To Uninstall paleomix on Ubuntu 22.04
To uninstall only the paleomix package we can use the following command:
sudo apt-get remove paleomix
Uninstall paleomix And Its Dependencies
To uninstall paleomix and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove paleomix
Remove paleomix Configurations and Data
To remove paleomix configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge paleomix
Remove paleomix configuration, data, and all of its dependencies
We can use the following command to remove paleomix configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge paleomix
References
Summary
In this tutorial we learn how to install paleomix package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.
