From mboxrd@z Thu Jan 1 00:00:00 1970 From: ludovic.courtes@inria.fr (Ludovic =?utf-8?Q?Court=C3=A8s?=) Subject: Re: [rb-general] Paper preprint: Reproducible genomics analysis pipelines with GNU Guix Date: Fri, 11 May 2018 10:10:19 +0200 Message-ID: <878t8qr4t0.fsf@inria.fr> References: <87604yndgh.fsf@elephly.net> <87o9ia49md.fsf@gnu.org> <87fu30fsra.fsf@elephly.net> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:38118) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1fH38F-000096-Df for guix-devel@gnu.org; Fri, 11 May 2018 04:10:28 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fH38E-0004XG-EX for guix-devel@gnu.org; Fri, 11 May 2018 04:10:27 -0400 In-Reply-To: <87fu30fsra.fsf@elephly.net> (Ricardo Wurmus's message of "Wed, 09 May 2018 23:01:29 +0200") List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: Ricardo Wurmus Cc: guix-devel , "guix-hpc@gnu.org" Hello! Ricardo Wurmus skribis: > Ludovic Court=C3=A8s 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 =E2=80=98configure.ac=E2=80=99 files without any l= ine 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 =E2=80=9Cconfigure.ac=E2=80=9D file would be of gr= eat help. In > general, independent of this particular use case. Perhaps we could add to Autoconf-Archive (if it doesn=E2=80=99t have such t= hings 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=E2=80=99t nee= d 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=E2=80=99d love to collaborate with other= users > of the GWL to see how far we can push it. Would be nice, indeed. Thanks, Ludo=E2=80=99.