From patchwork Mon Nov 29 15:48:27 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 34875 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 4386A27BBE9; Mon, 29 Nov 2021 15:49:15 +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 E5A0927BBEB for ; Mon, 29 Nov 2021 15:49:14 +0000 (GMT) Received: from localhost ([::1]:55662 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1mriu2-0006Ap-3W for patchwork@mira.cbaines.net; Mon, 29 Nov 2021 10:49:14 -0500 Received: from eggs.gnu.org ([209.51.188.92]:33084) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mritr-0006AD-7v for guix-patches@gnu.org; Mon, 29 Nov 2021 10:49:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:55681) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1mritq-0006CT-WF for guix-patches@gnu.org; Mon, 29 Nov 2021 10:49:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1mritq-00034q-Uq for guix-patches@gnu.org; Mon, 29 Nov 2021 10:49:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#52091] [PATCH v2 1/1] gnu: Add ccwl. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 29 Nov 2021 15:49:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 52091 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 52091@debbugs.gnu.org Cc: Arun Isaac Received: via spool by 52091-submit@debbugs.gnu.org id=B52091.163820091611756 (code B ref 52091); Mon, 29 Nov 2021 15:49:02 +0000 Received: (at 52091) by debbugs.gnu.org; 29 Nov 2021 15:48:36 +0000 Received: from localhost ([127.0.0.1]:38990 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mritQ-00033S-5Z for submit@debbugs.gnu.org; Mon, 29 Nov 2021 10:48:36 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:43538) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mritM-000339-EK for 52091@debbugs.gnu.org; Mon, 29 Nov 2021 10:48:34 -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: References:In-Reply-To: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:List-Id:List-Help: List-Unsubscribe:List-Subscribe:List-Post:List-Owner:List-Archive; bh=bBL5mFxsRp/4/9qNzGttk/gJcBOWTEv/K82F4u3FYOM=; b=TBRI/FOeRaGVvmOdjyBLXz4GrO 3vaxnj2qyJNUbo1GusiPmjkKxOx/G7k3WzULNx9sEJwGvT/Lvz9KyLkPYPozDptcpkqZetvxYaSP0 sIl3khSUpscDTmivDcKB0Ct1pDDbwXeqg7nClHRwNpmpTIkinyPtoBK1BSxXLLMI6qGozrktpMO9V LHaRUiPiHT10ndbQ7TcKK7wiiuMWsTgH8AWFa0hTQjW9AMk04ccFc/B7xSVXjbdXnFyWY51cmMX+V 2jELP5L8FjqFvv6M4N/aOACpbUknVx1A022qaq4b6TpIQDMGpVIlvvaesTUcnnQgY9bsASvUR9Z4T 9Z0VShbw==; Received: from [192.168.2.1] (port=15226 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 1mritJ-0002sE-G4; Mon, 29 Nov 2021 21:18:29 +0530 From: Arun Isaac Date: Mon, 29 Nov 2021 21:18:27 +0530 Message-Id: <20211129154827.18303-2-arunisaac@systemreboot.net> X-Mailer: git-send-email 2.34.0 In-Reply-To: <20211129154827.18303-1-arunisaac@systemreboot.net> References: <20211129154827.18303-1-arunisaac@systemreboot.net> MIME-Version: 1.0 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 | 53 +++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 67335daead..364fbad2cf 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 +15887,55 @@ (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 + #:modules (((guix build guile-build-system) + #:select (target-guile-effective-version)) + ,@%gnu-build-system-modules) + #:imported-modules ((guix build guile-build-system) + ,@%gnu-build-system-modules) + #:phases + (modify-phases %standard-phases + (add-after 'install 'wrap + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (effective-version (target-guile-effective-version))) + (wrap-program (string-append out "/bin/ccwl") + `("GUILE_LOAD_PATH" prefix + (,(string-append out "/share/guile/site/" effective-version) + ,(getenv "GUILE_LOAD_PATH"))) + `("GUILE_LOAD_COMPILED_PATH" prefix + (,(string-append out "/lib/guile/" effective-version "/site-ccache") + ,(getenv "GUILE_LOAD_COMPILED_PATH")))))))))) + (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+)))