How To Install metaphlan on Debian 12
Introduction
In this tutorial we learn how to install metaphlan
on Debian 12.
What is metaphlan
metaphlan is:
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.
MetaPhlAn relies on ~1.1M unique clade-specific marker genes (the latest marker information file mpa_v31_CHOCOPhlAn_201901_marker_info.txt.bz2 can be found here) identified from ~100,000 reference genomes (~99,500 bacterial and archaeal and ~500 eukaryotic), allowing:
- unambiguous taxonomic assignments;
- accurate estimation of organismal relative abundance;
- species-level resolution for bacteria, archaea, eukaryotes and viruses;
- strain identification and tracking
- orders of magnitude speedups compared to existing methods.
- metagenomic strain-level population genomics
There are three methods to install metaphlan
on Debian 12. We can use apt-get
, apt
and aptitude
. In the following sections we will describe each method. You can choose one of them.
Install metaphlan Using apt-get
Update apt database with apt-get
using the following command.
sudo apt-get update
After updating apt database, We can install metaphlan
using apt-get
by running the following command:
sudo apt-get -y install metaphlan
Install metaphlan Using apt
Update apt database with apt
using the following command.
sudo apt update
After updating apt database, We can install metaphlan
using apt
by running the following command:
sudo apt -y install metaphlan
Install metaphlan 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 Debian. Update apt database with aptitude
using the following command.
sudo aptitude update
After updating apt database, We can install metaphlan
using aptitude
by running the following command:
sudo aptitude -y install metaphlan
How To Uninstall metaphlan on Debian 12
To uninstall only the metaphlan
package we can use the following command:
sudo apt-get remove metaphlan
Uninstall metaphlan And Its Dependencies
To uninstall metaphlan
and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove metaphlan
Remove metaphlan Configurations and Data
To remove metaphlan
configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge metaphlan
Remove metaphlan configuration, data, and all of its dependencies
We can use the following command to remove metaphlan
configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge metaphlan
Dependencies
metaphlan have the following dependencies:
- python3-biom-format
- python3-biopython
- python3-dendropy
- python3-numpy
- python3-pandas
- python3-pysam
- python3-requests
- python3-scipy
- python3
References
Summary
In this tutorial we learn how to install metaphlan
package on Debian 12 using different package management tools: apt
, apt-get
and aptitude
.