How To Install paleomix on Kali Linux
Introduction
In this tutorial we learn how to install paleomix
on Kali Linux.
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 Kali Linux. 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 on Kali Linux first since aptitude is usually not installed by default on Kali Linux. 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 Kali Linux
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 Kali Linux, we can use the command below:
sudo apt-get -y autoremove paleomix
Remove paleomix Configurations and Data
To remove paleomix
configuration and data from Kali Linux 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
Dependencies
paleomix have the following dependencies:
- python3-coloredlogs
- python3-configargparse
- python3-pysam
- python3-ruamel.yaml
- python3-setproctitle
- python3
References
Summary
In this tutorial we learn how to install paleomix
package on Kali Linux using different package management tools: apt
, apt-get
and aptitude
.