How To Install clstr_reduce on Ubuntu 22.04

One-liner install command

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

sudo apt-get update && sudo apt -y install cd-hit

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

What is clstr_reduce and what are the ways to install it?

Before beginning this tutorial, you will need access to a server or computer running Ubuntu 22.04. This guide was written specifically with a server running Ubuntu 22.04 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 clstr_reduce on Ubuntu 22.04. 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 clstr_reduce 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 clstr_reduce using apt by running the following command:

sudo apt -y install cd-hit

Install clstr_reduce using apt

Because clstr_reduce is available in Ubuntu 22.04’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 clstr_reduce using apt by running the following command:

sudo apt -y install cd-hit

Install clstr_reduce 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 22.04. Update apt database with aptitude using the following command.

sudo aptitude update

After updating aptitude database, You can install clstr_reduce by running the following command:

sudo aptitude -y install cd-hit

How to upgrade (update) a single package clstr_reduce 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 clstr_reduce, e.g. single package, you should use the following format with the apt-get command/apt command:

sudo apt-get --only-upgrade install cd-hit

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 cd-hit

How To Uninstall clstr_reduce from Ubuntu 22.04

To uninstall only the clstr_reduce package you can execute the following command:

sudo apt-get remove cd-hit

Uninstall clstr_reduce and all its dependencies

To uninstall clstr_reduce and its dependencies that are no longer needed by Ubuntu 22.04, you can use the command below:

sudo apt-get -y autoremove cd-hit

Remove clstr_reduce with all configurations and data

To remove clstr_reduce configuration and data from your system you can run the following purge command:

sudo apt-get -y purge cd-hit

Remove clstr_reduce completely (configurations, data and all of its dependencies)

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

sudo apt-get -y autoremove --purge cd-hit

Extra info and code examples

cd-hit contains a number of programs designed to quickly group sequences. cd-hit groups proteins into clusters that meet a user-defined similarity threshold. cd-hit-est is similar to cd-hit, but designed to group nucleotide sequences (without introns). cd-hit-est-2d is similar to cd-hit-2d but designed to compare two nucleotide datasets. A number of other related programs are also in this package. Please see the cd-hit user manual, also part of this package, for further information.

Conclusion

You now have a full guide on how to install clstr_reduce using apt, apt-get and aptitude tools. Also, we showed how to update as a single package and different ways to uninstall the clstr_reduce from Ubuntu 22.04.

See also: