How To Install TransDecoder.Predict on CentOS 8

One-liner Install Command

If you are only interested in the installation command, here is a quick answer for you:

sudo yum makecache && sudo yum -y install transdecoder

sudo dnf makecache && sudo dnf -y install transdecoder

But if you are interested in the details with step-by-step instructions, the following information will be helpful.

What is TransDecoder.Predict and How to Install It?

First things first, you will need access to a server or computer running CentOS 8. This guide was written specifically with a server running CentOS 8 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 CentOS 8. 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 on CentOS 8 using dnf

First, update dnf packages database with dnf by running the next command:

sudo dnf makecache --refresh

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

sudo dnf -y install transdecoder

Install TransDecoder.Predict on CentOS 8 using yum

Because TransDecoder.Predict is available in CentOS 8’s default repositories, it is possible to install it from these repositories using the yum packaging system.

To begin, update local packages database with yum using the following command.

sudo yum makecache --refresh

Now can install TransDecoder.Predict package on your server/computer by running the following command:

sudo yum -y install transdecoder

How to upgrade (update) a single package TransDecoder.Predict using yum?

To update all the packages available on the system:

yum update

If you want to update a specific package like TransDecoder.Predict in this example you should use the following command:

yum update transdecoder

To downgrade a package to an earlier version:

yum downgrade transdecoder

How to Upgrade TransDecoder.Predict on CentOS 8 with dnf?

When you run the dnf update, all system packages with available updates are updated. However, if you want to upgrade a single package, then you would have to pass the package name as the argument to the dnf update command.

dnf update transdecoder

How To remove TransDecoder.Predict from CentOS 8

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

sudo dnf remove 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 dnf and yum package managers. Also, we showed how to update manually as a single package and different ways to uninstall the TransDecoder.Predict from CentOS 8.

See also: