How To Install libgkarrays-dev on Debian 9

In this tutorial we learn how to install libgkarrays-dev on Debian 9. libgkarrays-dev is library to query large collection of NGS sequences (development)

Introduction

In this tutorial we learn how to install libgkarrays-dev on Debian 9.

What is libgkarrays-dev

libgkarrays-dev is:

Gk-arrays are provided as a simple-to-use C++ library dedicated to queries on large collection of sequences as produced by high-throughput sequencers (e.g. HiSeq 2000 from Illumina, 454 from Roche).

Gk-arrays index k-mers of reads and allows one to answer different queries on that read collection (e.g. how many reads share this k-mer? where does this k-mer occur in the read collection?).

Gk-arrays consist of a space-efficient alternative to hash tables while being similar in terms of query times.

This is the development library for libgkarrays.

There are three methods to install libgkarrays-dev 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 libgkarrays-dev Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install libgkarrays-dev

Install libgkarrays-dev Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install libgkarrays-dev

Install libgkarrays-dev 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 libgkarrays-dev using aptitude by running the following command:

sudo aptitude -y install libgkarrays-dev

How To Uninstall libgkarrays-dev on Debian 9

To uninstall only the libgkarrays-dev package we can use the following command:

sudo apt-get remove libgkarrays-dev

Uninstall libgkarrays-dev And Its Dependencies

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

sudo apt-get -y autoremove libgkarrays-dev

Remove libgkarrays-dev Configurations and Data

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

sudo apt-get -y purge libgkarrays-dev

Remove libgkarrays-dev configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge libgkarrays-dev

Dependencies

libgkarrays-dev have the following dependencies:

References

Summary

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