How To Install cwltool 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 cwltool

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

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

sudo apt -y install cwltool

Install cwltool using apt

Because cwltool 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 cwltool using apt by running the following command:

sudo apt -y install cwltool

Install cwltool 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 cwltool by running the following command:

sudo aptitude -y install cwltool

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

sudo apt-get --only-upgrade install cwltool

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 cwltool

How To Uninstall cwltool from Ubuntu 22.04

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

sudo apt-get remove cwltool

Uninstall cwltool and all its dependencies

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

sudo apt-get -y autoremove cwltool

Remove cwltool with all configurations and data

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

sudo apt-get -y purge cwltool

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

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

sudo apt-get -y autoremove --purge cwltool

Extra info and code examples

This is the reference implementation of the Common Workflow Language standards. The CWL open standards are for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, Physics, and Chemistry. The CWL reference implementation (cwltool) is intended to be feature complete and to provide comprehensive validation of CWL files as well as provide other tools related to working with CWL descriptions.

Conclusion

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

See also: