Qiime2 on Windows Subsystem for Linux

Hi guys, actually im working with qiime2 on WSL but cant find a “tutorial” to install it, i know its simple but for someone new could be nice to find this kind of info.

First, install Windows Subsystem for Linux (WSL).

Open Windows Power Shell in Admin Mode and type in the console:

Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Windows-Subsystem-Linux

Then, restart your computer and from the Windows store install your desired Linux distro or just Ubuntu, then open it to finish the installation.

then, proceed to download miniconda with command wget:
(If your distro don’t have wget, type: $ conda install wget)

example: wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh (the link may vary)

we can get the link from the miniconda page, right click on the version you wish to download and then copy link

Once donwloaded the file, install it with command bash:

example: bash Miniconda3-latest-Linux-x86_64.sh (the file may vary)

just follow the instructions that appear in the console.

With everything prepared, we must get Qiime2, just need to follow the instructions in the Qiime2 Page.


NOTE: this page may vary depending on the versión of Qiime2 you want to install.

Once installed, we need a “share folder” between WSL and W10, it is not recommended to just enter to the WSL files and drag wat whe want, so…

In our WSL console, create a folder or directory (for example directory named sharew), once inside this directory type:

explorer.exe .

its important to not avoid the space and point at the end, this command opens the Windows explorer in the location typed (directory sharew), we can get this directory into “rapid acces” for an easy file share between w10 and our WSL, with this, we have everything ready to work!

IMPORTANT: ALWAYS open your WSL console before manipulating your shared directory / folder (no need to enter in to the folder in the console, just have it open).

comments and gramatic corrections are welcome


Hey, many thanks for this description!

Can I ask how you handle visualizations?

Since i want to avoid installing a VM, i am also using qiime2 on WSL. But i haven’t really found a comfortable solution for using visualizations from WSL. Sharing the .qzv files to window works of course, but if possible i would like to use the command qiime tools view somefile.qzv from WSL.
I have an Xserver and Xming set up and can run GUI apps from WSL, but this command does not connect.

Anyone any Ideas?

Thanks in advance

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I use the shared folder to acces the files and visualizate them on Windows, i havent find a way to visualizate them directly on WSL, que all i can find Is the Xserver and Xming option. If you find a solution could you share It here? ill be looking for one too.