How To Install positionDB 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 meryl

sudo dnf makecache && sudo dnf -y install meryl

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

What is positionDB 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 positionDB 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 positionDB 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 positionDB using dnf by running the following command:

sudo dnf -y install meryl

Install positionDB on CentOS 8 using yum

Because positionDB 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 positionDB package on your server/computer by running the following command:

sudo yum -y install meryl

How to upgrade (update) a single package positionDB using yum?

To update all the packages available on the system:

yum update

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

yum update meryl

To downgrade a package to an earlier version:

yum downgrade meryl

How to Upgrade positionDB 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 meryl

How To remove positionDB from CentOS 8

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

sudo dnf remove meryl

Extra info and code examples

meryl computes the kmer content of genomic sequences. Kmer content is represented as a list of kmers and the number of times each occurs in the input sequences. The kmer can be restricted to only the forward kmer, only the reverse kmer, or the canonical kmer (lexicographically smaller of the forward and reverse kmer at each location). Meryl can report the histogram of counts, the list of kmers and their counts, or can perform mathematical and set operations on the processed data files. This package is part of the Kmer suite.

Conclusion

You now have a full guide on how to install positionDB using dnf and yum package managers. Also, we showed how to update manually as a single package and different ways to uninstall the positionDB from CentOS 8.

See also: