From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:470:142:3::10]:36544) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1ibqvl-0003pq-Ng for gwl-devel@gnu.org; Mon, 02 Dec 2019 14:00:22 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ibqvk-00014i-5r for gwl-devel@gnu.org; Mon, 02 Dec 2019 14:00:21 -0500 Received: from mail-qt1-x82f.google.com ([2607:f8b0:4864:20::82f]:37701) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1ibqvk-00014W-10 for gwl-devel@gnu.org; Mon, 02 Dec 2019 14:00:20 -0500 Received: by mail-qt1-x82f.google.com with SMTP id w47so860958qtk.4 for ; Mon, 02 Dec 2019 11:00:19 -0800 (PST) MIME-Version: 1.0 References: In-Reply-To: From: zimoun Date: Mon, 2 Dec 2019 20:00:07 +0100 Message-ID: Subject: Re: How do I support building a guix package over multiple machines in a cloud environment? Content-Type: text/plain; charset="UTF-8" List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: gwl-devel-bounces+kyle=kyleam.com@gnu.org Sender: "gwl-devel" To: Josh Marshall Cc: gwl-devel@gnu.org Hi (again) Josh :-) On Mon, 2 Dec 2019 at 19:38, Josh Marshall wrote: > He uses it as a bioinformatics workflow to generate some analysis. It GWL should work for this use case. o/ > Is this kind of use case supported? If so, how so? Is nextflow not > practical to keep? Please, someone catch me up here so I can start to > write code to help him out. If this goes well, my company could > integrate for gwl/guix in our work, which would be amazing. Netxflow [1] is a Domain Specific Language (DSL): you write "rules" and how these rules are combined together. In the bioinformatics field, Snakemake [2] seems more popular. Other alternatives are CWL [3], WDL [4], etc. Basically, you describe: - what is the inputs - what is the outputs - how to process the inputs to produce the outputs You can find examples there [*]. It uses the WISP syntax [5] but it perfectly works with a Scheme-syntax if you prefer parenthesis. ;-) [*] https://guixwl.org/ However, you should be interested by this blog post [#] by Pjotr using Guix and CWL and other niceties! [#] https://hpc.guix.info/blog/2019/01/creating-a-reproducible-workflow-with-cwl/ AFAIK, Nextflow is not yet packaged in Guix. One direction is to package it and then use the workflow described in Nextflow DSL in the spirit of [#]. One other direction is to rewrite the workflow using the GWL DSL. It depends a bit on what is your final aim. Hope that helps. simon [1] https://www.nextflow.io/ [2] https://snakemake.readthedocs.io/en/stable/ [3] https://www.commonwl.org/ [4] http://www.openwdl.org/ [5] https://srfi.schemers.org/srfi-119/srfi-119.html