How To Install libhtsjdk-java on Debian 9

In this tutorial we learn how to install libhtsjdk-java on Debian 9. libhtsjdk-java is Java API for high-throughput sequencing data (HTS) formats

Introduction

In this tutorial we learn how to install libhtsjdk-java on Debian 9.

What is libhtsjdk-java

libhtsjdk-java is:

HTSJDK is an implementation of a unified Java library for accessing common file formats, such as SAM (Sequence Alignment/Map) and VCF, used for high-throughput sequencing data. There are also an number of useful utilities for manipulating HTS data.

There are three methods to install libhtsjdk-java on Debian 9. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install libhtsjdk-java Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install libhtsjdk-java using apt-get by running the following command:

sudo apt-get -y install libhtsjdk-java

Install libhtsjdk-java Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install libhtsjdk-java using apt by running the following command:

sudo apt -y install libhtsjdk-java

Install libhtsjdk-java 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 libhtsjdk-java using aptitude by running the following command:

sudo aptitude -y install libhtsjdk-java

How To Uninstall libhtsjdk-java on Debian 9

To uninstall only the libhtsjdk-java package we can use the following command:

sudo apt-get remove libhtsjdk-java

Uninstall libhtsjdk-java And Its Dependencies

To uninstall libhtsjdk-java and its dependencies that are no longer needed by Debian 9, we can use the command below:

sudo apt-get -y autoremove libhtsjdk-java

Remove libhtsjdk-java Configurations and Data

To remove libhtsjdk-java configuration and data from Debian 9 we can use the following command:

sudo apt-get -y purge libhtsjdk-java

Remove libhtsjdk-java configuration, data, and all of its dependencies

We can use the following command to remove libhtsjdk-java configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge libhtsjdk-java

Dependencies

libhtsjdk-java have the following dependencies:

References

Summary

In this tutorial we learn how to install libhtsjdk-java package on Debian 9 using different package management tools: apt, apt-get and aptitude.