How To Install libhts3 on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
2 minutes • 422 words
Introduction
In this tutorial we learn how to install libhts3 on Ubuntu.
What is libhts3
libhts3 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.
There are three methods to install libhts3 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 libhts3 Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install libhts3 using apt-get by running the following command:
sudo apt-get -y install libhts3
Install libhts3 Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install libhts3 using apt by running the following command:
sudo apt -y install libhts3
Install libhts3 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 libhts3 using aptitude by running the following command:
sudo aptitude -y install libhts3
How To Uninstall libhts3 on Ubuntu
To uninstall only the libhts3 package we can use the following command:
sudo apt-get remove libhts3
Uninstall libhts3 And Its Dependencies
To uninstall libhts3 and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove libhts3
Remove libhts3 Configurations and Data
To remove libhts3 configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge libhts3
Remove libhts3 configuration, data, and all of its dependencies
We can use the following command to remove libhts3 configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge libhts3
Dependencies
libhts3 have the following dependencies:
References
Summary
In this tutorial we learn how to install libhts3 package on Ubuntu using different package management tools: apt, apt-get and aptitude.