How To Install vg on Ubuntu 20.04
Introduction
In this tutorial we learn how to install vg
on Ubuntu 20.04.
What is vg
vg is:
variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods
Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of:
- nodes, which are labeled by sequences and ids
- edges, which connect two nodes via either of their respective ends
- paths, describe genomes, sequence alignments, and annotations (such as gene models and transcripts) as walks through nodes connected by edges
This model is similar to a number of sequence graphs that have been used in assembly and multiple sequence alignment. Paths provide coordinate systems relative to genomes encoded in the graph, allowing stable mappings to be produced even if the structure of the graph is changed.
There are three methods to install vg
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 vg Using apt-get
Update apt database with apt-get
using the following command.
sudo apt-get update
After updating apt database, We can install vg
using apt-get
by running the following command:
sudo apt-get -y install vg
Install vg Using apt
Update apt database with apt
using the following command.
sudo apt update
After updating apt database, We can install vg
using apt
by running the following command:
sudo apt -y install vg
Install vg 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 vg
using aptitude
by running the following command:
sudo aptitude -y install vg
How To Uninstall vg on Ubuntu 20.04
To uninstall only the vg
package we can use the following command:
sudo apt-get remove vg
Uninstall vg And Its Dependencies
To uninstall vg
and its dependencies that are no longer needed by Ubuntu 20.04, we can use the command below:
sudo apt-get -y autoremove vg
Remove vg Configurations and Data
To remove vg
configuration and data from Ubuntu 20.04 we can use the following command:
sudo apt-get -y purge vg
Remove vg configuration, data, and all of its dependencies
We can use the following command to remove vg
configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge vg
References
Summary
In this tutorial we learn how to install vg
package on Ubuntu 20.04 using different package management tools: apt
, apt-get
and aptitude
.