How To Install jellyfish-examples on Ubuntu 18.04
Introduction
In this tutorial we learn how to install jellyfish-examples on Ubuntu 18.04.
What is jellyfish-examples
jellyfish-examples is:
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the “compare-and-swap” CPU instruction to increase parallelism.
JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the “jellyfish dump” command.
This package contains examples to test the package
There are three methods to install jellyfish-examples on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install jellyfish-examples Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install jellyfish-examples using apt-get by running the following command:
sudo apt-get -y install jellyfish-examples
Install jellyfish-examples Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install jellyfish-examples using apt by running the following command:
sudo apt -y install jellyfish-examples
Install jellyfish-examples 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 Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install jellyfish-examples using aptitude by running the following command:
sudo aptitude -y install jellyfish-examples
How To Uninstall jellyfish-examples on Ubuntu 18.04
To uninstall only the jellyfish-examples package we can use the following command:
sudo apt-get remove jellyfish-examples
Uninstall jellyfish-examples And Its Dependencies
To uninstall jellyfish-examples and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove jellyfish-examples
Remove jellyfish-examples Configurations and Data
To remove jellyfish-examples configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge jellyfish-examples
Remove jellyfish-examples configuration, data, and all of its dependencies
We can use the following command to remove jellyfish-examples configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge jellyfish-examples
References
Summary
In this tutorial we learn how to install jellyfish-examples package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
