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Containerized workflow in containerized processes

From: Simon Tournier
Subject: Containerized workflow in containerized processes
Date: Mon, 13 Mar 2023 13:50:32 +0100


>From thread in guix-devel:

        Using Guix inside a Guix container
        Sat, 18 Feb 2023 11:01:50 +0100

The use-case “Containerized workflow in containerized processes” appears
to me interesting. :-)

It is almost done by design with GWL, no?

-------------------- Start of forwarded message --------------------
From: Konrad Hinsen <>
To: Simon Tournier <>, Guix Devel <>
Subject: Re: Using Guix inside a Guix container
Date: Sat, 18 Feb 2023 10:21:52 +0100

Hi Simon,

> Which part of Guix do you need inside the containerized shell that you
> cannot do outside?

That's not the right question. There's always a way to do what I want to
do outside. But that may be very inconvenient.

> Considering your use-case with Snakemake, what I am doing is to wrap
> each rule with one containerized Guix shell which controls the
> permissions, rule by rule; or a big containerized shell:
>     guix shell -C -m manifest.scm --expose=…

Nice example. I do the same: "guix shell" in every rule. Then I add
stuff to my Snakefile, which is a Python script after all. For example,
I import pandas to read a data frame from which I construct my workflow.
Now I am at the point where I'd like to run snakemake itself in a
container, to manage the dependencies of my Snakefile. In fact, given
that I have workflows that depend on specific Snakemake versions, I'd
really like to run Snakemake in a container all the time, even without
additional dependencies.

Without nested containers, I have to go through all the rules, collect
the packages from their manifest files (or command line), and add them
to the container in which I run the whole workflow. Possible, but not

Another example: I run command-line programs from my Pharo image, and I
have developed the habit of doing this always through Guix. The
advantage is that my Pharo code becomes portable: it depends on Guix,
but not on my profile.

But if I want, one day, to move on to a full Guix system, I have to run
Pharo in a container with LFS simulation. And then all my command line
shell-outs will break.

Both examples are about composing tools freely, without worrying if they
use Guix internally or now.


-------------------- End of forwarded message --------------------


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