How To Install python3-cyvcf2 on Ubuntu 20.04
Introduction
In this tutorial we learn how to install python3-cyvcf2
on Ubuntu 20.04.
What is python3-cyvcf2
python3-cyvcf2 is:
This modules allows fast parsing of VCF and BCF including region-queries with Python. This is essential for efficient analyses of nucleotide variation with Python on high-throughput sequencing data.
cyvcf2 is a cython wrapper around htslib. Attributes like variant.gt_ref_depths return a numpy array directly so they are immediately ready for downstream use.
This package installs the library for Python 3.
There are three methods to install python3-cyvcf2
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 python3-cyvcf2 Using apt-get
Update apt database with apt-get
using the following command.
sudo apt-get update
After updating apt database, We can install python3-cyvcf2
using apt-get
by running the following command:
sudo apt-get -y install python3-cyvcf2
Install python3-cyvcf2 Using apt
Update apt database with apt
using the following command.
sudo apt update
After updating apt database, We can install python3-cyvcf2
using apt
by running the following command:
sudo apt -y install python3-cyvcf2
Install python3-cyvcf2 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 python3-cyvcf2
using aptitude
by running the following command:
sudo aptitude -y install python3-cyvcf2
How To Uninstall python3-cyvcf2 on Ubuntu 20.04
To uninstall only the python3-cyvcf2
package we can use the following command:
sudo apt-get remove python3-cyvcf2
Uninstall python3-cyvcf2 And Its Dependencies
To uninstall python3-cyvcf2
and its dependencies that are no longer needed by Ubuntu 20.04, we can use the command below:
sudo apt-get -y autoremove python3-cyvcf2
Remove python3-cyvcf2 Configurations and Data
To remove python3-cyvcf2
configuration and data from Ubuntu 20.04 we can use the following command:
sudo apt-get -y purge python3-cyvcf2
Remove python3-cyvcf2 configuration, data, and all of its dependencies
We can use the following command to remove python3-cyvcf2
configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge python3-cyvcf2
References
Summary
In this tutorial we learn how to install python3-cyvcf2
package on Ubuntu 20.04 using different package management tools: apt
, apt-get
and aptitude
.