How To Install cwl-utils on Debian 12
Introduction
In this tutorial we learn how to install cwl-utils on Debian 12.
What is cwl-utils
cwl-utils is:
cwl-docker-extract - cache or pre-pull all software container images referenced in a CWL CommandLineTool or CWL Workflow (including all referenced CommandLineTools and sub-Workflows and so on).
cwl-cite-extract - prints all software packages found (recursively) in the specified CWL document.
cwl-expression-refactor - refactors CWL documents so that any CWL Expression evaluations are separate steps (either CWL ExpressionTools or CWL CommandLineTools). This allows execution by CWL engines that do not want to support inline expression evaluation outside of concrete steps, or do not want to directly support CWL’s optional InlineJavascriptRequirement at all.
cwl-graph-split - Splits a packed CWL document file into multiple files. Packed CWL documents use the $graph construct to contain multiple CWL Process objects (Workflow, CommandLineTool, ExpressionTool, Operation). Typically packed CWL documents contain a CWL Workflow under the name “main” and the workflow steps (including any sub-workflows) [requires cwlformat].
cwl-normalizer - Normalizes a CWL document all its dependencies into a single JSON format CWL document, upgrading to CWL v1.2, as needed. Can optionally refactor CWL Expressions into separate steps in the manner of cwl-expression-refactor [requires cwl-upgrader].
There are three methods to install cwl-utils on Debian 12. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install cwl-utils Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install cwl-utils using apt-get by running the following command:
sudo apt-get -y install cwl-utils
Install cwl-utils Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install cwl-utils using apt by running the following command:
sudo apt -y install cwl-utils
Install cwl-utils 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 cwl-utils using aptitude by running the following command:
sudo aptitude -y install cwl-utils
How To Uninstall cwl-utils on Debian 12
To uninstall only the cwl-utils package we can use the following command:
sudo apt-get remove cwl-utils
Uninstall cwl-utils And Its Dependencies
To uninstall cwl-utils and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove cwl-utils
Remove cwl-utils Configurations and Data
To remove cwl-utils configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge cwl-utils
Remove cwl-utils configuration, data, and all of its dependencies
We can use the following command to remove cwl-utils configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge cwl-utils
Dependencies
cwl-utils have the following dependencies:
References
Summary
In this tutorial we learn how to install cwl-utils package on Debian 12 using different package management tools: apt, apt-get and aptitude.
