How To Install metaphlan2-data on Ubuntu 20.04
Introduction
In this tutorial we learn how to install metaphlan2-data
on Ubuntu 20.04.
What is metaphlan2-data
metaphlan2-data is:
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. From version 2.0, MetaPhlAn is also able to identify specific strains (in the not-so-frequent cases in which the sample contains a previously sequenced strains) and to track strains across samples for all species.
MetaPhlAn 2.0 relies on ~1M unique clade-specific marker genes (the marker information file can be found at src/utils/markers_info.txt.bz2 or here) identified from ~17,000 reference genomes (~13,500 bacterial and archaeal, ~3,500 viral, and ~110 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
This package contains the data for metaphlan2.
There are three methods to install metaphlan2-data
on Ubuntu 20.04. We can use apt-get
, apt
and aptitude
. In the following sections we will describe each method. You can choose one of them.
Install metaphlan2-data Using apt-get
Update apt database with apt-get
using the following command.
sudo apt-get update
After updating apt database, We can install metaphlan2-data
using apt-get
by running the following command:
sudo apt-get -y install metaphlan2-data
Install metaphlan2-data Using apt
Update apt database with apt
using the following command.
sudo apt update
After updating apt database, We can install metaphlan2-data
using apt
by running the following command:
sudo apt -y install metaphlan2-data
Install metaphlan2-data 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 metaphlan2-data
using aptitude
by running the following command:
sudo aptitude -y install metaphlan2-data
How To Uninstall metaphlan2-data on Ubuntu 20.04
To uninstall only the metaphlan2-data
package we can use the following command:
sudo apt-get remove metaphlan2-data
Uninstall metaphlan2-data And Its Dependencies
To uninstall metaphlan2-data
and its dependencies that are no longer needed by Ubuntu 20.04, we can use the command below:
sudo apt-get -y autoremove metaphlan2-data
Remove metaphlan2-data Configurations and Data
To remove metaphlan2-data
configuration and data from Ubuntu 20.04 we can use the following command:
sudo apt-get -y purge metaphlan2-data
Remove metaphlan2-data configuration, data, and all of its dependencies
We can use the following command to remove metaphlan2-data
configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge metaphlan2-data
References
Summary
In this tutorial we learn how to install metaphlan2-data
package on Ubuntu 20.04 using different package management tools: apt
, apt-get
and aptitude
.