How To Install seqan-needle on Debian 12
Introduction
In this tutorial we learn how to install seqan-needle on Debian 12.
What is seqan-needle
seqan-needle is:
Needle is a tool for semi-quantitative analysis of very large collections of nucleotide sequences.
Needle stores its data in multiple interleaved Bloom filter, a fast and space efficient probabilistic data structure and uses a windowing scheme (also called minimisers) to reduce the amount of data to store. How many interleaved Bloom filter are used is defined by the user. Each interleaved Bloom filter has a so called expression threshold and stores minimisers with an occurrence greater than or equal to its own expression threshold and smaller than the next biggest expression threshold (if there is no bigger expression threshold, all greater than or equal to the threshold are stored). These expression thresholds are then used during the query (called estimate) to approximate the expression values of given transcripts.
There are three methods to install seqan-needle 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 seqan-needle Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install seqan-needle using apt-get by running the following command:
sudo apt-get -y install seqan-needle
Install seqan-needle Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install seqan-needle using apt by running the following command:
sudo apt -y install seqan-needle
Install seqan-needle 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 seqan-needle using aptitude by running the following command:
sudo aptitude -y install seqan-needle
How To Uninstall seqan-needle on Debian 12
To uninstall only the seqan-needle package we can use the following command:
sudo apt-get remove seqan-needle
Uninstall seqan-needle And Its Dependencies
To uninstall seqan-needle and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove seqan-needle
Remove seqan-needle Configurations and Data
To remove seqan-needle configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge seqan-needle
Remove seqan-needle configuration, data, and all of its dependencies
We can use the following command to remove seqan-needle configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge seqan-needle
Dependencies
seqan-needle have the following dependencies:
References
Summary
In this tutorial we learn how to install seqan-needle package on Debian 12 using different package management tools: apt, apt-get and aptitude.
