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GWL bash-minimal masks input bash

From: Liliana Marie Prikler
Subject: GWL bash-minimal masks input bash
Date: Wed, 06 Apr 2022 10:38:51 +0200
User-agent: Evolution 3.42.1

Hi scientific Guix,

I have a scientific workflow that depends on a bash script using an
extension.  (I wish I did not.)  Said script is the least common
denominator working on all systems that have some basic utilities, and
needs therefore not consider the reproducibility of its inputs (it is
assumed, that those are up to date).  However, at least on my personal
machine I want to ensure the reproducibility of the entire workflow,
including the invocation of said script.

I wrote a GWL workflow that calls the script, but due to the extension
the script actually fails in the GWL context.  This is because GWL's
process->script unconditionally conses bash-minimal to the process
inputs.  It should probably check whether a bash input already exists
or alternatively just append (list (bash-minimal)) instead.

For those in a similar situation as I am needing a fix, the following
works for me: instead of calling "bash" inside the workflow's inline
code, I specify
--8<---------------cut here---------------start------------->8---
      package-file bash "bin/bash"
--8<---------------cut here---------------end--------------->8---
and use {{values}} instead of "bash" to call my script.  (Don't forget
to add bash to your inputs, because package-file does not guarantee
existence of the file). 


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