How To Install vg-docs on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 449 words
Introduction
In this tutorial we learn how to install vg-docs on Ubuntu.
What is vg-docs
vg-docs 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.
This package provides the documentation
There are three methods to install vg-docs on Ubuntu. 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-docs 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-docs using apt-get by running the following command:
sudo apt-get -y install vg-docs
Install vg-docs Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install vg-docs using apt by running the following command:
sudo apt -y install vg-docs
Install vg-docs 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-docs using aptitude by running the following command:
sudo aptitude -y install vg-docs
How To Uninstall vg-docs on Ubuntu
To uninstall only the vg-docs package we can use the following command:
sudo apt-get remove vg-docs
Uninstall vg-docs And Its Dependencies
To uninstall vg-docs and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove vg-docs
Remove vg-docs Configurations and Data
To remove vg-docs configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge vg-docs
Remove vg-docs configuration, data, and all of its dependencies
We can use the following command to remove vg-docs configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge vg-docs
Dependencies
vg-docs have the following dependencies:
References
Summary
In this tutorial we learn how to install vg-docs package on Ubuntu using different package management tools: apt, apt-get and aptitude.