From: Ricardo Wurmus <rekado@elephly.net>
To: Liliana Marie Prikler <liliana.prikler@ist.tugraz.at>
Cc: gwl-devel@gnu.org
Subject: Re: GWL bash-minimal masks input bash
Date: Tue, 12 Jul 2022 21:05:32 +0200 [thread overview]
Message-ID: <878royxi5n.fsf@elephly.net> (raw)
In-Reply-To: <ecdc5e7164349541cba7ddfef15eb239e9f2cb17.camel@ist.tugraz.at>
Hi Liliana,
> 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.
Would appending bash-minimal really help? Does it really give
preference to your bash when resolving conflicts as it builds the
profile?
Not sure how we should check for the presence of a package providing a
shell. We can check for certain packages by name, of course, but it
doesn’t feel right to me.
Any other ideas how to accommodate the need to swap out the package
providing a shell?
> 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
>
> values
> run-with-store
> open-connection
> package-file bash "bin/bash"
>
> 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).
That’s an interesting solution. Thanks for sharing it.
--
Ricardo
next prev parent reply other threads:[~2022-07-12 19:09 UTC|newest]
Thread overview: 5+ messages / expand[flat|nested] mbox.gz Atom feed top
2022-04-06 8:38 GWL bash-minimal masks input bash Liliana Marie Prikler
2022-05-02 9:33 ` zimoun
2022-05-02 10:42 ` Liliana Marie Prikler
2022-07-12 19:05 ` Ricardo Wurmus [this message]
2022-07-13 5:55 ` Liliana Marie Prikler
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