How To Install remove_short_seqs 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 cct

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

What is remove_short_seqs 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 remove_short_seqs 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 remove_short_seqs 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 remove_short_seqs using apt by running the following command:

sudo apt -y install cct

Install remove_short_seqs using apt

Because remove_short_seqs 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 remove_short_seqs using apt by running the following command:

sudo apt -y install cct

Install remove_short_seqs 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 remove_short_seqs by running the following command:

sudo aptitude -y install cct

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

sudo apt-get --only-upgrade install cct

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 cct

How To Uninstall remove_short_seqs from Ubuntu 22.04

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

sudo apt-get remove cct

Uninstall remove_short_seqs and all its dependencies

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

sudo apt-get -y autoremove cct

Remove remove_short_seqs with all configurations and data

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

sudo apt-get -y purge cct

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

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

sudo apt-get -y autoremove --purge cct

Extra info and code examples

The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences of interest to existing genomes or sequence collections. The comparisons are conducted using BLAST, and the BLAST results are presented in the form of graphical maps that can also show sequence features, gene and protein names, COG category assignments, and sequence composition characteristics. CCT can generate maps in a variety of sizes, including 400 Megapixel maps suitable for posters. Comparisons can be conducted within a particular species or genus, or all available genomes can be used. The entire map creation process, from downloading sequences to redrawing zoomed maps, can be completed easily using scripts included with the CCT. User-defined features or analysis results can be included on maps, and maps can be extensively customized. To simplify program setup, a CCT virtual machine that includes all dependencies preinstalled is available. Detailed tutorials illustrating the use of CCT are included with the CCT documentation.

Conclusion

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

See also: