How To Install hts-nim-tools on Debian 12
Introduction
In this tutorial we learn how to install hts-nim-tools on Debian 12.
What is hts-nim-tools
hts-nim-tools is:
This package provides several tools that (at least at the time of their creation) provide functionalities beyond the routine provided by samtools and other reverse dependencies of the htslib.
These new tools are ?? bam-filter : filter BAM/CRAM/SAM files with a simple expression language ?? count-reads: count BAM/CRAM reads in regions given in a BED file ?? vcf-check : check regions of a VCF against a background for missing chunks
and yes, as the name suggests, these tools are all implemented in nim, using the nim-hts (upstream: hts-nim) wrapper for the htslib.
There are three methods to install hts-nim-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 hts-nim-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 hts-nim-tools using apt-get by running the following command:
sudo apt-get -y install hts-nim-tools
Install hts-nim-tools Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install hts-nim-tools using apt by running the following command:
sudo apt -y install hts-nim-tools
Install hts-nim-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 hts-nim-tools using aptitude by running the following command:
sudo aptitude -y install hts-nim-tools
How To Uninstall hts-nim-tools on Debian 12
To uninstall only the hts-nim-tools package we can use the following command:
sudo apt-get remove hts-nim-tools
Uninstall hts-nim-tools And Its Dependencies
To uninstall hts-nim-tools and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove hts-nim-tools
Remove hts-nim-tools Configurations and Data
To remove hts-nim-tools configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge hts-nim-tools
Remove hts-nim-tools configuration, data, and all of its dependencies
We can use the following command to remove hts-nim-tools configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge hts-nim-tools
Dependencies
hts-nim-tools have the following dependencies:
References
Summary
In this tutorial we learn how to install hts-nim-tools package on Debian 12 using different package management tools: apt, apt-get and aptitude.
