Docker image with QIIME and Jupyter

Hi! I am wondering if there is a Docker image (qiime + jupyterlab)? If not, is there a Dockerfile for the qiime2 Docker image? I am working with folks at CyVerse to get the latest version updated to run on our Atmosphere. Thanks!

Have you seen this?

https://docs.qiime2.org/2018.11/install/virtual/docker/

That one doesn’t have QIIME2 and Jupyter Lab together in a dockerfile.

The beauty of Docker is that you can layer images together! Take the QIIME 2 image as a base, then layer on the changes for JupyterLab. You can do that by building a new Dockerfile that indicates the QIIME 2 image as the FROM value:

FROM qiime2/core:2018.11
FROM jupyter/minimal-notebook

...

Hope that helps! :t_rex:

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That can be a bit complicated to use, see: https://blog.alexellis.io/mutli-stage-docker-builds/

I would probably recommend just installing QIIME 2 ontop of the Jupyter base image. Jupyter should have the more complex configuration anyhow and it comes with conda.

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