Hello! Ricardo Wurmus <rek...@elephly.net> skribis:
> Ludovic Courtès <ludovic.cour...@inria.fr> writes: [...] >> Given the intended audience, I wonder how we could provide a simpler >> path to achieve the same goal. It could be a set of Autoconf macros >> leading to high-level ‘configure.ac’ files without any line of shell >> code, or it could be Guix interpreting a top-level .scm or JSON file, >> both of which would ideally be easier to write for bioinformaticians. > > I think a higher level “configure.ac” file would be of great help. In > general, independent of this particular use case. Perhaps we could add to Autoconf-Archive (if it doesn’t have such things already) macros to deal with the R and Python stuff you had to deal with? And then publish a simple template that people could use as a starting point. > There is a danger in pushing all of this work to Guix, though. One of > the great features of the Autotools suite is that users don’t need to > know about it. If we assume that users have Guix (which in our paper we > only strongly encourage) we might as well have implemented the whole > pipeline using the Guix Workflow Language. This is, of course, a valid > option, but the goal of the paper was to demonstrate a more general > claim and approach to designing pipelines. I wanted to encourage > pipeline developers to treat their pipeline as a first-class package, > not as some glue code that binds together tools in a specially crafted > runtime environment. Yes, that makes sense. > I think that this alternative is worth exploring, though. Building a > complex pipeline with the Guix Workflow Language that addresses both > deployment and execution order would be an interesting project; it would > also be good to look into ways to make such a workflow available to > users who do not have the ability or intention to install Guix. An easy > way is to bundle up the whole environment as one giant container blob, > but I think we can do better. I’d love to collaborate with other users > of the GWL to see how far we can push it. Would be nice, indeed. Thanks, Ludo’.
