How To Install ncbi-entrez-direct on Kali Linux
Introduction
In this tutorial we learn how to install ncbi-entrez-direct on Kali Linux.
What is ncbi-entrez-direct
ncbi-entrez-direct is:
Entrez Direct (EDirect) is an advanced method for accessing NCBI’s set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a terminal window or script. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.
EDirect also provides an argument-driven function that simplifies the extraction of data from document summaries or other results that are returned in structured XML format. This can eliminate the need for writing custom software to answer ad hoc questions. Queries can move seamlessly between EDirect commands and UNIX utilities or scripts to perform actions that cannot be accomplished entirely within Entrez.
There are three methods to install ncbi-entrez-direct on Kali Linux. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install ncbi-entrez-direct Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get updateAfter updating apt database, We can install ncbi-entrez-direct using apt-get by running the following command:
sudo apt-get -y install ncbi-entrez-directInstall ncbi-entrez-direct Using apt
Update apt database with apt using the following command.
sudo apt updateAfter updating apt database, We can install ncbi-entrez-direct using apt by running the following command:
sudo apt -y install ncbi-entrez-directInstall ncbi-entrez-direct Using aptitude
If you want to follow this method, you might need to install aptitude on Kali Linux first since aptitude is usually not installed by default on Kali Linux. Update apt database with aptitude using the following command.
sudo aptitude updateAfter updating apt database, We can install ncbi-entrez-direct using aptitude by running the following command:
sudo aptitude -y install ncbi-entrez-directHow To Uninstall ncbi-entrez-direct on Kali Linux
To uninstall only the ncbi-entrez-direct package we can use the following command:
sudo apt-get remove ncbi-entrez-directUninstall ncbi-entrez-direct And Its Dependencies
To uninstall ncbi-entrez-direct and its dependencies that are no longer needed by Kali Linux, we can use the command below:
sudo apt-get -y autoremove ncbi-entrez-directRemove ncbi-entrez-direct Configurations and Data
To remove ncbi-entrez-direct configuration and data from Kali Linux we can use the following command:
sudo apt-get -y purge ncbi-entrez-directRemove ncbi-entrez-direct configuration, data, and all of its dependencies
We can use the following command to remove ncbi-entrez-direct configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge ncbi-entrez-directDependencies
ncbi-entrez-direct have the following dependencies:
References
Summary
In this tutorial we learn how to install ncbi-entrez-direct package on Kali Linux using different package management tools: apt, apt-get and aptitude.