Windows Users (WSL)

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Just kidding (sort of). Follow the steps below.

Creating a Nextflow Environment

Please follow the steps outlined in the following tutorial: Setting up a Nextflow environment on Windows 10.

  1. Powershell

  2. WSL2

  3. Windows terminal

  4. Docker

  5. VS Code (optional)

  6. Nextflow

  7. Git

Please make sure that you install nextflow v21.04.1. When following the tutorial, substitute the following during the nextflow installation:

$ wget https://github.com/nextflow-io/nextflow/releases/download/v21.04.1/nextflow

$ chmod 777 ./nextflow

$ mv ./nextflow /usr/local/bin/

$ nextflow -v

Note

If the path /usr/local/bin does not exist, move the executable to /usr/bin/ instead.

Installing Singularity

The above tutorial does not cover singularity installations. Please follow this tutorial to install singularity: `using singularity on windows with WSL2<https://www.blopig.com/blog/2021/09/using-singularity-on-windows-with-wsl2/>`_.

When you reach the step to download the tarball from GitHub, use the same version as ubuntu users for the workshop:

$ export VERSION=3.8.4 && \
wget https://github.com/apptainer/singularity/releases/download/v${VERSION}/singularity-${VERSION}.tar.gz && \
tar -xzf singularity-${VERSION}.tar.gz && \
cd singularity-${VERSION}

Windows users in the class - please help each other during the installation steps. I do not have a Windows partition on my laptop and cannot troubleshoot any issues you may encounter.

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