How To Install joingenes 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 augustus

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

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

sudo apt -y install augustus

Install joingenes using apt

Because joingenes 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 joingenes using apt by running the following command:

sudo apt -y install augustus

Install joingenes 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 joingenes by running the following command:

sudo aptitude -y install augustus

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

sudo apt-get --only-upgrade install augustus

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 augustus

How To Uninstall joingenes from Ubuntu 22.04

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

sudo apt-get remove augustus

Uninstall joingenes and all its dependencies

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

sudo apt-get -y autoremove augustus

Remove joingenes with all configurations and data

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

sudo apt-get -y purge augustus

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

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

sudo apt-get -y autoremove --purge augustus

Extra info and code examples

AUGUSTUS is a software for gene prediction in eukaryotic genomic sequences that is based on a generalized hidden Markov model (HMM), a probabilistic model of a sequence and its gene structure. After learning gene structures from a reference annotation, AUGUSTUS uses the HMM to recognize genes in a new sequence and annotates it with the regions of identified genes. External hints, e.g. from RNA sequencing, EST or protein alignments etc. can be used to guide and improve the gene finding process. The result is the set of most likely gene structures that comply with all given user constraints, if such gene structures exist. AUGUSTUS already includes prebuilt HMMs for many species, as well as scripts to train custom models using annotated genomes.

Conclusion

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

See also: