I have installed Docker and downloaded two distributions (Amplicon & Pathogenome). Both show up under Containers as expected. However, when I attempt to start either, they both immediately exit. I have attempted to run the “Test your install” command for both in PowerShell but receive the following errors:
I am unsure how to proceed so that the distributions are usable.
@tomahawk1527, I'm not familiar with PowerShell, so this may be the wrong track, but the first thing I would try is adapting that command so that it's all on one line (rather than using \ to break lines). I am wondering if PowerShell is interpreting the \ different than other shells that we use.
Specifically, I would try running the following:
docker run -v $(pwd):/data -it quay.io/qiime2/amplicon:2025.10 qiime info
In running the single line command in PowerShell, it still gives the error of “invalid reference format”.
Running it in CMD gives the error “docker: Error response from daemon: create (pwd): "(pwd)" includes invalid characters for a local volume name, only "[a-zA-Z0-9][a-zA-Z0-9_.-]" are allowed. If you intended to pass a host directory, use absolute path"
Running it in the WSL window gives the error "It looks like you have tried to invoke the docker CLI from the docker-desktop WSL2 distribution. This is not supported. Please invoke the docker CLI from the Windows Command Prompt, PowerShell, or other compatible terminals."
I think I see - it looks like the issue is that we're suggesting a Linux-style absolute path for the -v argument (-v $(pwd):/data), but you need to specify a Linux/macOS style path:
This should likely be replaced with something like -v C:\my-data, if you have a directory called my-data at the root of your C: drive. (Here is an article that talks about absolute paths on Windows versus Linux/macOS if this concept is new to you.)
This is indeed a new concept for me as I have no working knowledge of QIIME, Docker, or Linux. But I've been tasked with installing QIIME distributions for a professor.
I am attempting to use the terminal built into Docker, but running that command with the changes you suggested still give the error "invalid reference format". And -v, -it, and qiime are not recognized.
This is one of those "I don't know what I don't know" things.
@tomahawk1527, the issue seems to be at the level of Docker (hence the: "docker: invalid reference format" error). Docker hasn't yet been able to load the QIIME 2 container. Do you have access at your institution to anyone who can provide Docker support for you? Alternatively, I'd do some googling for this specific error - a quick search turned up this discussion.
The discussion you linked to had the solution I needed for the terminal window errors. Copying the script you originally shared, but replacing (pwd) with {pwd} allowed the terminal inside Docker to spit out system versions, installed plugins, directory location, and configuration source. I am now just trying to figure out how to run the containers without it exiting immediately after starting.
As a follow-up to my previous reply, I have created a volume in Docker and attempted to import the Amplicon and Pathogenome local images, but receive the follow error:
Error invoking remote method 'volumes.importFromImage__wrapped': Error: An object could not be cloned.
Any suggestions would be appreciated. I attempted to search the forum for that specific issue, but could not seem to find a post on the topic.
This was me 12 years ago!
Docker might be a bit technical if you don't already know how to use Linux...
How many machines are you putting Qiime2 on?
Are these all running Windows 10 or MacOS or something else?
(I run Qiime2 on WSL2 on Windows and that was pretty easy to set up)
Just a single machine running Windows 11.
Cool
Here my current setup (2025) if you want to us that for inspiration:
)After I got WSL installed (it defaults to Ubuntu Linux), I started the WSL terminal to make sure it was working and I could run linux commands.
Then I did that final step of connecting vscode to WSL.
Then I opened up vscode, connected to Ubuntu, and installed conda and Qiime2 like it was a Linux virtual machine (because it is a Linux vm).
Let me know if you try this setup and if it works for you!
There is a lot to learn in Linux and bioinformatics in general so take your time. We are here to help you get Qiime2 running and more!
In trying to connect VSC to WSL, I'm prompted to create an Alpine container and run apk update and apk add libstdc++. I've figured out how to do the first part of that, but in running that command in the Alpine terminal, I receive the following errors:
ERROR: Unable to lock database: Permission denied
ERROR: Failed to open apk database: Permission denied
Is this something you would be willing to walk me through on a call or through TeamViewer?
If you got WSL installed, you don't need VS Code at all, you can run commands directly in the WSL Ubuntu terminal. (I'm not sure how you found Alpine, but that's not getting us closer to Qiime2.)
In WSL2, were you able to install mininconda?
Looks like you can't save files to the folder you are in.
Try going to your home directory simply by running
cd
to go to your own home directory.
Then try the download again!
That made all the difference. I was able to install conda and then the amplicon distribution right after. Now it's just a matter of installing for a professor and hoping they know how to use the program. Thank you.
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