How To Install fitgcp on Debian 9
Introduction
In this tutorial we learn how to install fitgcp on Debian 9.
What is fitgcp
fitgcp is:
Genome coverage, the number of sequencing reads mapped to a position in a genome, is an insightful indicator of irregularities within sequencing experiments. While the average genome coverage is frequently used within algorithms in computational genomics, the complete information available in coverage profiles (i.e. histograms over all coverages) is currently not exploited to its full extent. Thus, biases such as fragmented or erroneous reference genomes often remain unaccounted for. Making this information accessible can improve the quality of sequencing experiments and quantitative analyses.
fitGCP is a framework for fitting mixtures of probability distributions to genome coverage profiles. Besides commonly used distributions, fitGCP uses distributions tailored to account for common artifacts. The mixture models are iteratively fitted based on the Expectation-Maximization algorithm.
There are three methods to install fitgcp 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 fitgcp Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install fitgcp using apt-get by running the following command:
sudo apt-get -y install fitgcp
Install fitgcp Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install fitgcp using apt by running the following command:
sudo apt -y install fitgcp
Install fitgcp 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 fitgcp using aptitude by running the following command:
sudo aptitude -y install fitgcp
How To Uninstall fitgcp on Debian 9
To uninstall only the fitgcp package we can use the following command:
sudo apt-get remove fitgcp
Uninstall fitgcp And Its Dependencies
To uninstall fitgcp and its dependencies that are no longer needed by Debian 9, we can use the command below:
sudo apt-get -y autoremove fitgcp
Remove fitgcp Configurations and Data
To remove fitgcp configuration and data from Debian 9 we can use the following command:
sudo apt-get -y purge fitgcp
Remove fitgcp configuration, data, and all of its dependencies
We can use the following command to remove fitgcp configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge fitgcp
Dependencies
fitgcp have the following dependencies:
References
Summary
In this tutorial we learn how to install fitgcp package on Debian 9 using different package management tools: apt, apt-get and aptitude.