How To Install libgenomicsdb0 on Debian 12

Learn how to install libgenomicsdb0 on Debian 12 with this tutorial. libgenomicsdb0 is sparse array storage library for genomics (shared libraries)

Introduction

In this tutorial we learn how to install libgenomicsdb0 on Debian 12.

What is libgenomicsdb0

libgenomicsdb0 is:

GenomicsDB is built on top of a htslib fork and an internal array storage system for importing, querying and transforming variant data. Variant data is sparse by nature (sparse relative to the whole genome) and using sparse array data stores is a perfect fit for storing such data.

The GenomicsDB stores variant data in a 2D array where:

  • Each column corresponds to a genomic position (chromosome + position);
  • Each row corresponds to a sample in a VCF (or CallSet in the GA4GH terminology);
  • Each cell contains data for a given sample/CallSet at a given position; data is stored in the form of cell attributes;
  • Cells are stored in column major order - this makes accessing cells with the same column index (i.e. data for a given genomic position over all samples) fast.
  • Variant interval/gVCF interval data is stored in a cell at the start of the interval. The END is stored as a cell attribute. For variant intervals (such as deletions and gVCF REF blocks), an additional cell is stored at the END value of the variant interval. When queried for a given genomic position, the query library performs an efficient sweep to determine all intervals that intersect with the queried position.

This package contains the shared library.

There are three methods to install libgenomicsdb0 on Debian 12. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install libgenomicsdb0 Using apt-get

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

sudo apt-get update

After updating apt database, We can install libgenomicsdb0 using apt-get by running the following command:

sudo apt-get -y install libgenomicsdb0

Install libgenomicsdb0 Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install libgenomicsdb0 using apt by running the following command:

sudo apt -y install libgenomicsdb0

Install libgenomicsdb0 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 libgenomicsdb0 using aptitude by running the following command:

sudo aptitude -y install libgenomicsdb0

How To Uninstall libgenomicsdb0 on Debian 12

To uninstall only the libgenomicsdb0 package we can use the following command:

sudo apt-get remove libgenomicsdb0

Uninstall libgenomicsdb0 And Its Dependencies

To uninstall libgenomicsdb0 and its dependencies that are no longer needed by Debian 12, we can use the command below:

sudo apt-get -y autoremove libgenomicsdb0

Remove libgenomicsdb0 Configurations and Data

To remove libgenomicsdb0 configuration and data from Debian 12 we can use the following command:

sudo apt-get -y purge libgenomicsdb0

Remove libgenomicsdb0 configuration, data, and all of its dependencies

We can use the following command to remove libgenomicsdb0 configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge libgenomicsdb0

Dependencies

libgenomicsdb0 have the following dependencies:

References

Summary

In this tutorial we learn how to install libgenomicsdb0 package on Debian 12 using different package management tools: apt, apt-get and aptitude.