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This is my first question on stackoverflow.

I want to use both ubuntu:18.04 and bioconductor/bioconductor_docker docker images to build a docker image for a nextflow pipeline using resources from both containers. I am not a software developer of any sort. Please help me with pointing me to an appropriate docker file or just how should I go about it.

I think some sort of multistage docker file should be a way to go, but not sure and any help would be great.

Rohit Gupta
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Vineet
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  • Just saying, but the Bioconductor image is based on (tracking it all back to the original template image) on the Ubuntu Docker image, so there is nothing on that Ubuntu image that would not be in the Bioc one. Long story: Bioconductor is based on Rocker-RStudio is based on R-Ver is based on Ubuntu. – ATpoint Apr 18 '23 at 16:13

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Welcome, Vineet

If you really want to combine two Docker images, and given that you have the Dockerfile for both images, a multi-stage build is the way to go. However, I wonder if that's really what you should be doing...

Though there could be cases where this is needed, the best practice is to have small and specific Docker images for your Nextflow processes. Ideally, every process would have a container image that has exactly what it needs, in a way that it's (1) fast to pull from a container hub, (2) fast to run, (3) fast to stop/exit, and (4) easy to debug when errors occur. If you have a large/multi-process image, you will run into issues in all these 4 things I mentioned above.

mribeirodantas
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