Installing CRISPResso2 on Windows via WSL

[kclem]

CRISPResso can't be installed directly onto a Windows machine because some of the tools called by CRISPResso (e.g. Flash and bowtie2) installations are complicated on Windows.

However, I run CRISPResso on Windows using the Windows Subsystem for Linux, which allows me to run linux and programs installed on linux, while still accessing my files on Windows. This can be accomplished through the following steps:

1. Install WSL

Follow these instructions:
https://docs.microsoft.com/en-us/windows/wsl/install

1. Open powershell

2. Run wsl --install

3. Restart your machine

This will install “Ubuntu” which is a type of linux, which you can then open up as a program.
Note that you must be running Windows 10 version 2004 and higher (Build 19041 and higher) or Windows 11 to install WSL.

2. Install anaconda into your WSL

Next, install anaconda using these instructions in the Ubuntu window: https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html

1. Open Ubuntu
   

2. Type wget [https://repo.anaconda.com/archive/Anaconda3-2021.11-Linux-x86_64.sh](https://repo.anaconda.com/archive/Anaconda3-2021.11-Linux-x86_64.sh)

3. Type bash Anaconda3-2021.11-Linux-x86_64.sh

Follow the instructions to complete installation of conda

3. Install CRISPResso

1. Finalize your conda installation by typing source ./bashrc
2. Install CRISPResso using conda:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

conda create -n crispresso2_env -c bioconda crispresso2

You should then be able to run CRISPResso.

File access

One of the great things about WSL is that you can access your local windows files from WSL, and vice versa. So to access your files on Ubuntu - or to copy input files to where you can see them on Ubuntu, open a File Explorer window, and in the top navigation bar type "Linux" and press Enter. Your files should be in Linux > Ubuntu > home > {username}.

You can also access your Windows drives and documents from WSL in the /mnt directory, so your documents in the c drive could be found via the paths: /mnt/c/Users/crispressouser/My\ Documents