Running Qiime 2 through Docker and opening images


I have completed the moving pictures tutorial by running qiime2/core:2019.10. After I completed the tutorial I typed “exit” then I typed "docker commit " and the numbers after “[email protected]” and When I type “docker image ls” I can see the new image from the tutorial I just ran and that it has a file size.

My question is: If I want to go back into the tutorial and open some files I had made during the analysis, how would I do that? Is it possible with the actions I took?

Any advice anyone can give would be invaluable. I am new to qiime and docker and not many tutorials cover what to do after you are done analyzing your data.

Thank you very much!

Hey @MattGlad!

This is probably unnecessary, since you can use “volumes” to save data to, instead of keeping it locked up in docker.

If you ran the command suggested on the docs, nothing:

docker run -t -i -v $(pwd):/data qiime2/core:2019.10 qiime

This will mount your current working directory to the /data dir inside the container - anything you create or manipulate in /data will be saved in your current working directory on your host machine.


Hi @thermokarst,

I think I understand now, some documents a colleague gave me did not include “/data” , so I assume that explains why these documents are not found on my host machine?

This is why I wanted to run the tutorial a few times so I was comfortable with everything.

Thank you very much for the speedy response and clarification!

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@thermokarst Sorry one more question,

When I run the command you provided:

I recieved the following error:
C:\Program Files\Docker\Docker\resources\bin\docker.exe: invalid reference format.
See ‘C:\Program Files\Docker\Docker\resources\bin\docker.exe run --help’.

I see this is a common error and all the solutions I see aren’t directly applicable to this situation. I am using windows PowerShell if that means anything.

Thanks again!

Hey there @MattGlad, this is a new error for me, too. A quick internet search yielded this post:

Since you’re running PowerShell, give this a shot:

 docker run -t -i -v ${PWD}:/data qiime2/core:2019.10 qiime

Hi @thermokarst,

That did the trick! thanks a lot for your help!



you need to use the same syntax for starting qiime and running it through a container in Docker, through PowerShell:

docker run --rm -it -u {id -u}:{id -g} -v ${PWD}:/data qiime2/core:2019.10 /bin/bash

Once you run this you can run the rest of the tutorial as it intends!

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