How To Install cwltool on Debian 10
Introduction
In this tutorial we learn how to install cwltool
on Debian 10.
What is cwltool
cwltool is:
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.
There are three methods to install cwltool
on Debian 10. 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 10
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 10, 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 10 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:
- python3-mypy
- python3-pkg-resources
- python3-prov
- python3-psutil
- python3-rdflib
- python3-requests
- python3-ruamel.yaml
- python3-schema-salad
- python3-shellescape
- python3-six
- python3-typing-extensions
- python3
References
Summary
In this tutorial we learn how to install cwltool
package on Debian 10 using different package management tools: apt
, apt-get
and aptitude
.