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Re: leaky pipelines and Guix

From: myglc2
Subject: Re: leaky pipelines and Guix
Date: Mon, 07 Mar 2016 18:21:08 -0500
User-agent: Gnus/5.13 (Gnus v5.13) Emacs/24.5 (gnu/linux)

address@hidden (Ludovic Courtès) writes:

> myglc2 <address@hidden> skribis:
>> address@hidden (Ludovic Courtès) writes:
> [...]
>>> 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))))
>> Sidebar:
>> - What is "biopipeline" above? A new guix command?
> Right.  Basically I was suggesting implementing the pipeline as a Scheme
> procedure (‘foo-pipeline’ above), and adding a command-line interface on
> top of it (‘guix biopipeline’.)
> This means that all inputs and outputs would go through the store, so
> you would get caching and all that for free.
> But I now understand that I was slightly off-topic.  ;-)

Thanks. Having built bespoke analysis pipelines for the last five years,
I find your idea intriguing. So my response to the original post was
slightly off-topic. also ;)

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