How To Install cwltool on Debian 9

In this tutorial we learn how to install cwltool on Debian 9. cwltool is Common workflow language reference implementation

Introduction

In this tutorial we learn how to install cwltool on Debian 9.

What is cwltool

cwltool is:

This is the reference implementation of the Common Workflow Language. It is intended to be feature complete and provide comprehensive validation of CWL files as well as provide other tools related to working with CWL.

This is written and tested for Python 2.7.

The reference implementation consists of two packages. The “cwltool” package is the primary Python module containing the reference implementation in the “cwltool” module and console executable by the same name.

The “cwl-runner” package is optional and provides an additional entry point under the alias “cwl-runner”, which is the implementation-agnostic name for the default CWL interpreter installed on a host.

There are three methods to install cwltool on Debian 9. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install cwltool Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install cwltool using apt-get by running the following command:

sudo apt-get -y install cwltool

Install cwltool Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We 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 Debian. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install cwltool using aptitude by running the following command:

sudo aptitude -y install cwltool

How To Uninstall cwltool on Debian 9

To uninstall only the cwltool package we can use the following command:

sudo apt-get remove cwltool

Uninstall cwltool And Its Dependencies

To uninstall cwltool and its dependencies that are no longer needed by Debian 9, we can use the command below:

sudo apt-get -y autoremove cwltool

Remove cwltool Configurations and Data

To remove cwltool configuration and data from Debian 9 we can use the following command:

sudo apt-get -y purge cwltool

Remove cwltool configuration, data, and all of its dependencies

We can use the following command to remove cwltool configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge cwltool

Dependencies

cwltool have the following dependencies:

References

Summary

In this tutorial we learn how to install cwltool package on Debian 9 using different package management tools: apt, apt-get and aptitude.