Re: leaky pipelines and Guix

[ludo@gnu.org (Ludovic Courtès)]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> So, how could I package something like that?  Is packaging the wrong
> approach here and should I really just be using “guix environment” to
> prepare a suitable environment, run the pipeline, and then exit?

Maybe packages are the wrong abstraction here?

IIUC, a pipeline is really a function that takes inputs and produces
output(s).  So it can definitely be modeled as a derivation.

Perhaps as a first step you could try and write a procedure and a CLI
around it that simply runs a given pipeline:

  $ guix biopipeline foo frog.dna human.dna
  …
  /gnu/store/…-freak.dna

The procedure itself would be along the lines of:

  (define (foo-pipeline input1 input2)
    (gexp->derivation "result"
                      #~(begin
                          (setenv "PATH" "/foo/bar")
                          (invoke-make-and-co #$input1 #$input2
                                              #$output))))

Once you’ve done this exercise for a couple of pipelines, perhaps you’ll
find a higher-level abstraction that captures properties common to all
bioinfo pipelines?

HTH,
Ludo’.