How To Install python-cyvcf2 on Debian 10
Introduction
In this tutorial we learn how to install python-cyvcf2 on Debian 10.
What is python-cyvcf2
python-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 2.
There are three methods to install python-cyvcf2 on Debian 10. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install python-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 python-cyvcf2 using apt-get by running the following command:
sudo apt-get -y install python-cyvcf2
Install python-cyvcf2 Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install python-cyvcf2 using apt by running the following command:
sudo apt -y install python-cyvcf2
Install python-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 Debian. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install python-cyvcf2 using aptitude by running the following command:
sudo aptitude -y install python-cyvcf2
How To Uninstall python-cyvcf2 on Debian 10
To uninstall only the python-cyvcf2 package we can use the following command:
sudo apt-get remove python-cyvcf2
Uninstall python-cyvcf2 And Its Dependencies
To uninstall python-cyvcf2 and its dependencies that are no longer needed by Debian 10, we can use the command below:
sudo apt-get -y autoremove python-cyvcf2
Remove python-cyvcf2 Configurations and Data
To remove python-cyvcf2 configuration and data from Debian 10 we can use the following command:
sudo apt-get -y purge python-cyvcf2
Remove python-cyvcf2 configuration, data, and all of its dependencies
We can use the following command to remove python-cyvcf2 configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge python-cyvcf2
Dependencies
python-cyvcf2 have the following dependencies:
References
Summary
In this tutorial we learn how to install python-cyvcf2 package on Debian 10 using different package management tools: apt, apt-get and aptitude.