CWL runner installation

The recommended CWL runner is cwltool, the reference implementation for the CWL standards.

The installation can be done following the guide here.

• Install Windows Subsystem for Linux from the Microsoft Store

• Install Debian from the Microsoft Store

• Set Debian as your default WSL 2 distro: wsl --set-default debian
• Install Docker Desktop for Windows
  • Start Docker Desktop and Navigate to Settings
  • Select "Use WSL 2 based engine" in the general tab and apply
  • Select "Enable Integration with my default distro" in the resources tab under WSL Integration
• Start WSL
• Follow the Instructions for Linux (Debian/Ubuntu)

• Run sudo apt-get update
• Install Python 3 if it is not already preinstalled sudo apt install python3
• Install python virtual environment sudo apt install python3.[your version here]-venv
• Create a virtual environment python3 -m venv env (named env here, name can vary)
• Activate the virtual environment source env/bin/activate
• Install cwltool with pip pip install cwltool

• If you are on Windows, start the WSL
• Activate the virtual environment source env/bin/activate
• Navigate to the results destination directory
• Run cwltool by specifying the CWL Workflow or CommandLineTool description file path and the (optional) inputs file path: cwltool path/to/cwlfile.cwl path/to/jobfile.yml (you can use relative or full paths)