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From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=)
Subject: Re: leaky pipelines and Guix
Date: Fri, 12 Feb 2016 15:04:56 +0100
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In-Reply-To: <idjtwli6s7w.fsf@bimsb-sys02.mdc-berlin.net> (Ricardo Wurmus's
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To: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Cc: help-guix@gnu.org

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 =E2=80=9Cguix environment=
=E2=80=9D 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
  =E2=80=A6
  /gnu/store/=E2=80=A6-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=E2=80=99ve done this exercise for a couple of pipelines, perhaps y=
ou=E2=80=99ll
find a higher-level abstraction that captures properties common to all
bioinfo pipelines?

HTH,
Ludo=E2=80=99.