How To Install entrez-phrase-search on Kali Linux

One-liner install command

For those in a hurry, here's a one-line installation command:

sudo apt-get update && sudo apt -y install ncbi-entrez-direct

But if you are interested in the detailed steps with descriptions, the following information is for you.

What is entrez-phrase-search and what are the ways to install it?

Before beginning this tutorial, you will need access to a server or computer running Kali Linux. This guide was written specifically with a server running Kali Linux in mind, although it should also work on older, supported versions of the operating system.

Also, make sure you are running a regular, non-root user with sudo privileges configured on your server. When you have an account available, log in as your non-root user to begin.

There are several ways to install entrez-phrase-search on Kali Linux. You can use (links are clickable):

In the following sections, we will describe each method in detail. You can choose one of them or refer to the recommended one.

Install entrez-phrase-search using apt-get

First, update apt database with apt-get using the following command.

sudo apt-get update

After updating apt-get database, You can install entrez-phrase-search using apt by running the following command:

sudo apt -y install ncbi-entrez-direct

Install entrez-phrase-search using apt

Because entrez-phrase-search is available in Kali Linux’s default repositories, it is possible to install it from these repositories using the apt packaging system.

To begin, update apt database with apt using the following command.

sudo apt update

After updating apt database, You can install entrez-phrase-search using apt by running the following command:

sudo apt -y install ncbi-entrez-direct

Install entrez-phrase-search 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 Kali Linux. Update apt database with aptitude using the following command.

sudo aptitude update

After updating aptitude database, You can install entrez-phrase-search by running the following command:

sudo aptitude -y install ncbi-entrez-direct

How to upgrade (update) a single package entrez-phrase-search using apt-get?

First, you will need to update packages index. Run update command as usual:

sudo apt-get update

Next, to upgrade only the entrez-phrase-search, e.g. single package, you should use the following format with the apt-get command/apt command:

sudo apt-get --only-upgrade install ncbi-entrez-direct

Note that this command will not install any new packages! If you wish to install the package if it doesn't exist you may leave out --only-upgrade part.

sudo apt-get install ncbi-entrez-direct

How To Uninstall entrez-phrase-search from Kali Linux

To uninstall only the entrez-phrase-search package you can execute the following command:

sudo apt-get remove ncbi-entrez-direct

Uninstall entrez-phrase-search and all its dependencies

To uninstall entrez-phrase-search and its dependencies that are no longer needed by Kali Linux, you can use the command below:

sudo apt-get -y autoremove ncbi-entrez-direct

Remove entrez-phrase-search with all configurations and data

To remove entrez-phrase-search configuration and data from your system you can run the following purge command:

sudo apt-get -y purge ncbi-entrez-direct

Remove entrez-phrase-search completely (configurations, data and all of its dependencies)

And lastly, you can run the next command to remove absolutely everything related to entrez-phrase-search package, e.g.: configurations, data and all of its dependencies. Just use this command:

sudo apt-get -y autoremove --purge ncbi-entrez-direct

Extra info and code examples

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.

Conclusion

You now have a full guide on how to install entrez-phrase-search using apt, apt-get and aptitude tools. Also, we showed how to update as a single package and different ways to uninstall the entrez-phrase-search from Kali Linux.

See also: