How To Install positionDB 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 meryl

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

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

sudo apt -y install meryl

Install positionDB using apt

Because positionDB 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 positionDB using apt by running the following command:

sudo apt -y install meryl

Install positionDB 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 positionDB by running the following command:

sudo aptitude -y install meryl

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

sudo apt-get --only-upgrade install meryl

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 meryl

How To Uninstall positionDB from Ubuntu 22.04

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

sudo apt-get remove meryl

Uninstall positionDB and all its dependencies

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

sudo apt-get -y autoremove meryl

Remove positionDB with all configurations and data

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

sudo apt-get -y purge meryl

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

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

sudo apt-get -y autoremove --purge 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 apt, apt-get and aptitude tools. Also, we showed how to update as a single package and different ways to uninstall the positionDB from Ubuntu 22.04.

See also: