How To Install TransDecoder.Predict on Ubuntu 21.04

One-liner install command

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

sudo apt-get update && sudo apt -y install transdecoder

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

What is TransDecoder.Predict and what are the ways to install it?

Before beginning this tutorial, you will need access to a server or computer running Ubuntu 21.04. This guide was written specifically with a server running Ubuntu 21.04 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 TransDecoder.Predict on Ubuntu 21.04. 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 TransDecoder.Predict 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 TransDecoder.Predict using apt by running the following command:

sudo apt -y install transdecoder

Install TransDecoder.Predict using apt

Because TransDecoder.Predict is available in Ubuntu 21.04’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 TransDecoder.Predict using apt by running the following command:

sudo apt -y install transdecoder

Install TransDecoder.Predict 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 21.04. Update apt database with aptitude using the following command.

sudo aptitude update

After updating aptitude database, You can install TransDecoder.Predict by running the following command:

sudo aptitude -y install transdecoder

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

sudo apt-get --only-upgrade install transdecoder

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 transdecoder

How To Uninstall TransDecoder.Predict from Ubuntu 21.04

To uninstall only the TransDecoder.Predict package you can execute the following command:

sudo apt-get remove transdecoder

Uninstall TransDecoder.Predict and all its dependencies

To uninstall TransDecoder.Predict and its dependencies that are no longer needed by Ubuntu 21.04, you can use the command below:

sudo apt-get -y autoremove transdecoder

Remove TransDecoder.Predict with all configurations and data

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

sudo apt-get -y purge transdecoder

Remove TransDecoder.Predict completely (configurations, data and all of its dependencies)

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

sudo apt-get -y autoremove --purge transdecoder

Extra info and code examples

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. TransDecoder identifies likely coding sequences based on the following criteria: * a minimum length open reading frame (ORF) is found in a transcript sequence * a log-likelihood score similar to what is computed by the GeneID software is > 0. * the above coding score is greatest when the ORF is scored in the 1st reading frame as compared to scores in the other 5 reading frames. * if a candidate ORF is found fully encapsulated by the coordinates of another candidate ORF, the longer one is reported. However, a single transcript can report multiple ORFs (allowing for operons, chimeras, etc). * optional the putative peptide has a match to a Pfam domain above the noise cutoff score.

Conclusion

You now have a full guide on how to install TransDecoder.Predict using apt, apt-get and aptitude tools. Also, we showed how to update as a single package and different ways to uninstall the TransDecoder.Predict from Ubuntu 21.04.

See also: