From patchwork Thu Nov 25 05:46:27 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 34802 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 8433C27BBEA; Thu, 25 Nov 2021 05:47:13 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 435DF27BBE9 for ; Thu, 25 Nov 2021 05:47:13 +0000 (GMT) Received: from localhost ([::1]:58852 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1mq7bE-0006Ki-CQ for patchwork@mira.cbaines.net; Thu, 25 Nov 2021 00:47:12 -0500 Received: from eggs.gnu.org ([209.51.188.92]:38790) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mq7b5-0006KJ-5P for guix-patches@gnu.org; Thu, 25 Nov 2021 00:47:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:44002) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1mq7b4-0007Iu-Sv for guix-patches@gnu.org; Thu, 25 Nov 2021 00:47:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1mq7b4-00084B-Le for guix-patches@gnu.org; Thu, 25 Nov 2021 00:47:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#52091] [PATCH] gnu: Add ccwl. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 25 Nov 2021 05:47:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 52091 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 52091@debbugs.gnu.org Cc: Arun Isaac X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.163781920430982 (code B ref -1); Thu, 25 Nov 2021 05:47:02 +0000 Received: (at submit) by debbugs.gnu.org; 25 Nov 2021 05:46:44 +0000 Received: from localhost ([127.0.0.1]:55548 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mq7am-00083e-4J for submit@debbugs.gnu.org; Thu, 25 Nov 2021 00:46:44 -0500 Received: from lists.gnu.org ([209.51.188.17]:60510) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mq7aj-00083U-K8 for submit@debbugs.gnu.org; Thu, 25 Nov 2021 00:46:43 -0500 Received: from eggs.gnu.org ([209.51.188.92]:38748) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mq7aj-0006If-3F for guix-patches@gnu.org; Thu, 25 Nov 2021 00:46:41 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:60392) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mq7ae-0007As-Lg for guix-patches@gnu.org; Thu, 25 Nov 2021 00:46:40 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Transfer-Encoding:MIME-Version: Message-Id:Date:Subject:Cc:To:From:Sender:Reply-To:Content-Type:Content-ID: Content-Description:Resent-Date:Resent-From:Resent-Sender:Resent-To:Resent-Cc :Resent-Message-ID:In-Reply-To:References:List-Id:List-Help:List-Unsubscribe: List-Subscribe:List-Post:List-Owner:List-Archive; bh=fjTNGa9oOTEovYMzKsgnKpL8fvmz2xzSAS9tW/kmP+k=; b=fn7nwUJQ0iIqBK7f5ZIz13Wt1J XSwGkgsGXGhmgSWc8UDf179aQ46r5QbRws7ApFebStgU6IOfvP7qrw9+4/fjmhBq2CVhAhaqrrqNW F/u4B+jes8b5vAKNeTSGlex5iMNkfCXmr20V5BA1GvYSroH32602/9mqePyfrWqaNLJas+yvlc+LP Qu7AgK71WCzxhPZ7bEhQj+OjoXm+DIscHc9vd7FByOpxeYqq/H1w4CgOxioPNQYdmjclmPZPOwlYW NopZBBlG+JG1MeHRA11LD8nIUf41eY3wnSJGQS/8GLMMSeAoJHUNi/CNo1M+YRKDl0NqnmgcDeMb7 MudBbH6A==; Received: from [192.168.2.1] (port=16236 helo=localhost.localdomain) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.95) (envelope-from ) id 1mq7aX-000ZII-5t; Thu, 25 Nov 2021 11:16:29 +0530 From: Arun Isaac Date: Thu, 25 Nov 2021 11:16:27 +0530 Message-Id: <20211125054627.24135-1-arunisaac@systemreboot.net> X-Mailer: git-send-email 2.34.0 MIME-Version: 1.0 Received-SPF: pass client-ip=139.59.75.54; envelope-from=arunisaac@systemreboot.net; helo=mugam.systemreboot.net X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (ccwl): New variable. --- gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 67335daead..ec34ff0916 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -142,6 +142,7 @@ (define-module (gnu packages bioinformatics) #:use-module (gnu packages ruby) #:use-module (gnu packages serialization) #:use-module (gnu packages shells) + #:use-module (gnu packages skribilo) #:use-module (gnu packages sphinx) #:use-module (gnu packages sqlite) #:use-module (gnu packages statistics) @@ -15886,3 +15887,37 @@ (define-public r-cytonorm control samples and applying quantile normalization on all markers of interest.") (license license:gpl2+)))) + +(define-public ccwl + (package + (name "ccwl") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://ccwl.systemreboot.net/releases/ccwl-" + version ".tar.lz")) + (sha256 + (base32 + "1ar8rfz3zrksgygrv67zv77y8gfvvz54zcs546jn6j28y20basla")))) + (build-system gnu-build-system) + (arguments + '(#:make-flags '("GUILE_AUTO_COMPILE=0"))) ; to prevent guild warnings + (inputs + `(("guile" ,guile-3.0) + ("guile-libyaml" ,guile-libyaml))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("lzip" ,lzip) + ;; To build documentation + ("cwltool" ,cwltool) + ("graphviz" ,graphviz) + ("skribilo" ,skribilo))) + (home-page "https://ccwl.systemreboot.net") + (synopsis "Concise common workflow language") + (description "The @acronym{ccwl, Concise Common Workflow Language} is a +concise syntax to express CWL workflows. ccwl is a compiler to generate CWL +workflows from concise descriptions in ccwl. It is implemented as an +@acronym{EDSL, Embedded Domain Specific Language} in the Scheme programming +language.") + (license license:gpl3+)))