How to use the QIIME 2 Galaxy container

The QIIME 2 Galaxy container enables you to use QIIME 2 through the Galaxy interface on your own hardware.

We recommend using either Podman or Docker. Before you jump in with QIIME 2, follow the “Get Started” (i.e., install) instructions for one or the other on the project’s website, and confirm that it’s working according to their instructions. (We don’t link to their instructions here so that we don’t send you to an outdated link).

Pulling the image and starting a container for the first time¶

After downloading and learning to use your chosen program, run the following command in a terminal:

docker container run \
 -d \
 -p 8080:80 \
 -p 8021:21 \
 -p 8020:20 \
 quay.io/qiime2/q2galaxy:<epoch>

docker container run \
 -d \
 -p 8080:80 \
 -p 8021:21 \
 -p 8020:20 \
 --platform "linux/amd64" \
 quay.io/qiime2/q2galaxy:<epoch>

podman container run \
 -d \
 -p 8080:80 \
 -p 8021:21 \
 -p 8020:20 \
 quay.io/qiime2/q2galaxy:<epoch>

podman container run \
 -d \
 -p 8080:80 \
 -p 8021:21 \
 -p 8020:20 \
 --platform "linux/amd64" \
 quay.io/qiime2/q2galaxy:<epoch>

You will need to replace <epoch> with the epoch you are targeting. To view available epochs, visit quay.io/qiime2/q2galaxy. The first time you run this command it will both pull the image and run a container off of it. Every subsequent time it will see that you already have the image and will create a new container without pulling it again.

Using the container¶

Once your container is running, open a web browser and navigate to http://localhost:8080. You will get a 502 error page while Galaxy is booting. Within a few minutes you should be able to refresh and see the Galaxy page. At this point you can use Galaxy as normal and your Galaxy History will be saved in the container you are running.