How to install QIIME2 through docker? Did you met this issue?

I am installing QIIME2 by many ways, all of them has a little success rate, I think something has been wrong with this developing platform, so I tried docker to install it.
Following the instructions by web pages, I just done it good at the beginning, but when I done this step:


It breaked by some unknown reasons:

So, how it works? Thank you!

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Hi @yangyue,

I suspect this is some kind of network error. I wouldn't worry about it because hello-world is not an important image.

Try pulling our image from quay.io with the command below and let us know what happens:

docker run \
  -v $(pwd):/data \
  -it quay.io/qiime2/amplicon:2025.7 \
  qiime info

If you run into a similar issue, could you describe your network situation in whatever detail you can? I assume we're working with the great firewall and a few other institution specific details based on the ubuntu mirrors in your screenshot.

3 Likes

Thank you!
I know it is one distribution of the webpage's default command (I stick on tired moshpit which I need now). I tired it many times, it has not successed yet, but the fourth pull was too large, about 3.998GB, could it be reduced? When there are many people using our net, the net flow will be breakened, retired many parts, so it will be retried so many times. :grinning_face: Could you tell me where is the location of QIIME2 services please๏ผŸ

Hey @yangyue,

Our different distributions of QIIME 2 include all of the necessary packages for each particular distribution, so there isn't a way for us to reduce the size of the moshpit image without removing necessary packages. Depending on the particular analysis you're running, you may be able to install the amplicon distribution instead of moshpit (it looks like in the past you've installed the QIIME 2 'core' distribution which is now the amplicon distribution). This will be a smaller image than the moshpit image.

3 Likes

I've installed the moshpit 2025.4 occasionally through WSL with once time, but may the dealing data of mine is so large, it suddenly occupied all of my disk speces when I run the "qiime tools import" command. So I have to remove it, then for another try. I've not installed it with a successful try yet since that uninstallation event, so I'm doubtful until now๐Ÿ˜‚. Did you think the past workshop about the docker may helpful?

I just have an expect on the moshpit, do you mean the amplicon is the easy installing distribution? :grinning_face:

I've just using your advice to install qiime2-amplicon:2025.7, it seems the pull has successed, but I don't know how to do the next step. Could you help me? :folded_hands:



Hello @yangyue,

It looks like the docker install was successful. This command:

docker run \
  -v $(pwd):/data \
  -it quay.io/qiime2/moshpit:2025.7 \
  qiime info

actually only tests the container by running the qiime info command and then exiting. If you want to interact with qiime2 through the command line run this:

docker run \
  -v $(pwd):/data \
  -it quay.io/qiime2/moshpit:2025.7 \
  /bin/bash

This will give you a shell in which you can run qiime2 commands.

However, I'm wondering if you were already in a docker container or other vm when running these docker commands because of the @qiime2-ubuntu command prompt. Is it possible you're a couple of levels deep in docker containers? (qiimeception)

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Please tell me where is a docker container? I've run it(the code I've shown above) on the latest verson of VirtualBox, but these days I removed the Box. I think it is hopeless, so I'm trying the 6.1 version of the VirtualBox for the above code youโ€™ve presented, but it failed :joy:. I'm just a newer for docker-QIIME2. I'm facing massive storage overflow problems when I run either a right or wrong command of the old version of QIIME2, so which environment do you think is the best for QIIME2-moshpit? :grinning_face:

Hello @yangyue,

Did you try the second command I posted? It looks like you have a docker container successfully installed and running. Now all you need to do is to use it so that you can use qiime2.

If that command is not working could you please post the error that you get?

Thank you,
I've just answered your question on the last reply, have you read it carefully?

Hello @yangyue,

If you did run the command that I suggested, and it failed, can you share the error it gave you so that we can troubleshoot?

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