Linux Subsystem on Windows Support?

I am running the Moving Pictures tutorial on Bash on Ubuntu/Windows 10 and got the same Errno 13 Permission denied at the denoising step that jbarlow submitted here. I read that Windows is not supported but hoped I could run qiime2 on Ubuntu. Is that not true?

Hi @lulabear! When you say “Bash on Ubuntu/Windows 10”, are you talking about the Windows Subsystem for Linux? If so, then this is a bit tricky — technically this is still Windows, which means we don’t support it (yet). We do support Ubuntu (well, Linux in general), but the WSL (which you are using) is a whole different beast, and isn’t quite the same thing as running Ubuntu natively. If you are planning on using Windows for your QIIME 2 analyses, the best we can offer right now is our official Docker container, or the Virtualbox VMs. Let us know if you have any questions! Thanks! :t_rex:

I installed Docker and ran the command to pull the 2017.8 core, then ran:

$ docker run -t -i -v $(pwd):/data qiime2/core:2017.8 qiime

This gave me the qiime cli parameter list I expected. But when I try to run a qiime command I get the error (for example):

bash: qiime: command not found

running: echo $0 I get: /usr/bin/bash instead of --bash

Can you tell me what I need to tweak to now use qiime within Docker?

Hi @lulabear, please take a look at this forum post for two general strategies for running QIIME 2 in Docker. Let us know if you have any questions - thanks! :t_rex:

I chose the interactive shell option which worked perfectly after consulting another docker forum post to add on mounting my much larger D drive to run in this container. Thanks for your help!

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