Re: GWL bash-minimal masks input bash

[Ricardo Wurmus]

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