How To Install htslib-test on Ubuntu 20.04
Introduction
In this tutorial we learn how to install htslib-test on Ubuntu 20.04.
What is htslib-test
htslib-test is:
HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang.
HTSlib implements a generalized BAM (binary SAM) index, with file extension ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent.
This package contains test files and scripts for the HTSlib.
There are three methods to install htslib-test 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 htslib-test Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install htslib-test using apt-get by running the following command:
sudo apt-get -y install htslib-test
Install htslib-test Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install htslib-test using apt by running the following command:
sudo apt -y install htslib-test
Install htslib-test 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 htslib-test using aptitude by running the following command:
sudo aptitude -y install htslib-test
How To Uninstall htslib-test on Ubuntu 20.04
To uninstall only the htslib-test package we can use the following command:
sudo apt-get remove htslib-test
Uninstall htslib-test And Its Dependencies
To uninstall htslib-test and its dependencies that are no longer needed by Ubuntu 20.04, we can use the command below:
sudo apt-get -y autoremove htslib-test
Remove htslib-test Configurations and Data
To remove htslib-test configuration and data from Ubuntu 20.04 we can use the following command:
sudo apt-get -y purge htslib-test
Remove htslib-test configuration, data, and all of its dependencies
We can use the following command to remove htslib-test configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge htslib-test
References
Summary
In this tutorial we learn how to install htslib-test package on Ubuntu 20.04 using different package management tools: apt, apt-get and aptitude.
