How To Install genomicsdb-tools on Debian 12
Introduction
In this tutorial we learn how to install genomicsdb-tools on Debian 12.
What is genomicsdb-tools
genomicsdb-tools 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 some tools to be run as executable files.
There are three methods to install genomicsdb-tools 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 genomicsdb-tools Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install genomicsdb-tools using apt-get by running the following command:
sudo apt-get -y install genomicsdb-tools
Install genomicsdb-tools Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install genomicsdb-tools using apt by running the following command:
sudo apt -y install genomicsdb-tools
Install genomicsdb-tools 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 genomicsdb-tools using aptitude by running the following command:
sudo aptitude -y install genomicsdb-tools
How To Uninstall genomicsdb-tools on Debian 12
To uninstall only the genomicsdb-tools package we can use the following command:
sudo apt-get remove genomicsdb-tools
Uninstall genomicsdb-tools And Its Dependencies
To uninstall genomicsdb-tools and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove genomicsdb-tools
Remove genomicsdb-tools Configurations and Data
To remove genomicsdb-tools configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge genomicsdb-tools
Remove genomicsdb-tools configuration, data, and all of its dependencies
We can use the following command to remove genomicsdb-tools configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge genomicsdb-tools
Dependencies
genomicsdb-tools have the following dependencies:
References
Summary
In this tutorial we learn how to install genomicsdb-tools package on Debian 12 using different package management tools: apt, apt-get and aptitude.