From unknown Sat Jun 14 03:57:23 2025 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 Content-Transfer-Encoding: 8bit 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-Spam-Score: -1.4 (-) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.4 (--) * 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+))) -- 2.34.0 From unknown Sat Jun 14 03:57:23 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#52091] [PATCH v2 0/1] Add ccwl References: <20211125054627.24135-1-arunisaac@systemreboot.net> In-Reply-To: <20211125054627.24135-1-arunisaac@systemreboot.net> 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=B52091.163820091611749 (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]:38988 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mritP-00033P-WC for submit@debbugs.gnu.org; Mon, 29 Nov 2021 10:48:36 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:43540) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mritM-00033A-FD 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: 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=NNTze74lbgYfGKLyCqVCKovjqKkbDsPe3Ha+BdzRQik=; b=ppQDJzzpmgGomhHHA5AcBTej+R 45GXKlGXcdONFI2d198+KdcpPcChtgMnPV3MU078WIf+u/gY82p6gC/c0ntLdyMBXKUFUCbpKUQCF 6u7NeMPsA4D1UDb+u0Az7BTZ7fWabJdTGrfBekKZrp6n9TUGI7zwMJB7JL/bBZsO5iTiMFBzxFGpN aDCGMs3PU2PnRq7OTHgg8gP0Bd2IuRdAxKk/iEVh2I5j65E7tQlQrfOSiNu/OMRVESGmu7A5AwKTw OmjCr6uQoEpYFSaepySGGF+OpDNp1QYNIo0lU/XHxGeNKoveJvE1LWz/XR3qNPXQeUMvbRgIh/xB+ h0rIfzqA==; 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-AO; Mon, 29 Nov 2021 21:18:29 +0530 From: Arun Isaac Date: Mon, 29 Nov 2021 21:18:26 +0530 Message-Id: <20211129154827.18303-1-arunisaac@systemreboot.net> X-Mailer: git-send-email 2.34.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hi, In the last patch, I forgot to wrap the ccwl executable. I have fixed this in the v2 patch. Regards, Arun Arun Isaac (1): gnu: Add ccwl. gnu/packages/bioinformatics.scm | 53 +++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) -- 2.34.0 From unknown Sat Jun 14 03:57:23 2025 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 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * 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+))) -- 2.34.0 From unknown Sat Jun 14 03:57:23 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#52091] [PATCH] gnu: Add ccwl. Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 09 Dec 2021 15:31:02 +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: Arun Isaac Cc: 52091@debbugs.gnu.org Received: via spool by 52091-submit@debbugs.gnu.org id=B52091.163906383224488 (code B ref 52091); Thu, 09 Dec 2021 15:31:02 +0000 Received: (at 52091) by debbugs.gnu.org; 9 Dec 2021 15:30:32 +0000 Received: from localhost ([127.0.0.1]:44571 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mvLNP-0006Ms-UG for submit@debbugs.gnu.org; Thu, 09 Dec 2021 10:30:32 -0500 Received: from eggs.gnu.org ([209.51.188.92]:40616) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mvLNO-0006Mh-M1 for 52091@debbugs.gnu.org; Thu, 09 Dec 2021 10:30:31 -0500 Received: from [2001:470:142:3::e] (port=47050 helo=fencepost.gnu.org) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mvLNI-0002MT-Ix; Thu, 09 Dec 2021 10:30:24 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-Version:In-Reply-To:Date:References:Subject:To: From; bh=SzlerI633homT0f0sDzqAZ5BvcnJdm/Mjyh2G3ym1Jc=; b=i2wjKVRGcIrP4gK92glu a3wEMjhv7mEbVACgJQhpx58H9/Ic0Oioj+pyFV4Ui2pihlkO0seKqJBkiDPLVKwR361gXEKMPD+JM U+wmmqQXMsWEo3pKJD11zxGGZZHa39WYm38HeWr/C/gvR5g9isg/Cy7JOSMpkZiWjInj7W/5B04AT vV4Rf8TdDbkBOKLSoOOTS7AnO7urlFdmkNuw1xHSJr5fExHW7uN7AdhGsffmUC5+gEx9owAvDmFO4 khOEAW2Bp/0m6C4eabvX/l+RnW0l2HOZtPowDb5U1PhvtSaZlRVQPnEUjdbJT71u2LMgV82qZVFA7 9/GQmuWdOS11zw==; Received: from [193.50.110.120] (port=41694 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mvLNI-0007cH-GE; Thu, 09 Dec 2021 10:30:24 -0500 From: Ludovic =?UTF-8?Q?Court=C3=A8s?= References: <20211129154827.18303-1-arunisaac@systemreboot.net> <20211129154827.18303-2-arunisaac@systemreboot.net> Date: Thu, 09 Dec 2021 16:30:22 +0100 In-Reply-To: <20211129154827.18303-2-arunisaac@systemreboot.net> (Arun Isaac's message of "Mon, 29 Nov 2021 21:18:27 +0530") Message-ID: <87fsr1g5ip.fsf_-_@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) Hello, Arun Isaac skribis: > * gnu/packages/bioinformatics.scm (ccwl): New variable. LGTM, go for it! Thanks, Ludo=E2=80=99. From unknown Sat Jun 14 03:57:23 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Arun Isaac Subject: bug#52091: closed (Re: bug#52091: [PATCH] gnu: Add ccwl.) Message-ID: References: <87czm4hiyf.fsf@systemreboot.net> <20211125054627.24135-1-arunisaac@systemreboot.net> X-Gnu-PR-Message: they-closed 52091 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 52091@debbugs.gnu.org Date: Fri, 10 Dec 2021 10:08:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1639130882-30581-1" This is a multi-part message in MIME format... ------------=_1639130882-30581-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #52091: [PATCH] gnu: Add ccwl. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 52091@debbugs.gnu.org. --=20 52091: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D52091 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1639130882-30581-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 52091-done) by debbugs.gnu.org; 10 Dec 2021 10:07:18 +0000 Received: from localhost ([127.0.0.1]:45572 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mvco9-0007wJ-QX for submit@debbugs.gnu.org; Fri, 10 Dec 2021 05:07:17 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:58494) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mvco6-0007w6-Gz for 52091-done@debbugs.gnu.org; Fri, 10 Dec 2021 05:07:16 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Type:MIME-Version:Message-ID:Date: References:In-Reply-To:Subject:Cc:To:From:Sender:Reply-To: Content-Transfer-Encoding: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=cQrm88EiDMMBcMYN1dIlytBwoc968aFug8lcZEiAIs8=; b=I/uym45yfSH9u2FoJG6ormOq0i urKpdhVp9RdFh29nqO3tWOLvD87w01i2SxdXUah9oiY0rdUc9eAFoff2Ct2vtMmSgQZ0J7izfkUdy dx81YqEO+MNGgepJMUmjzM+VwU8+9j3XlRJNV1kP2AccoqHUuvcZX2sbwJAVCLkOPYr5kkvTHGqGt C2hwec3e3930Tl4oLEHg71YpVeVqaXBQ5A3a/8QgRI6Ntj1gVnOCKn6hOwS+K0vxmTaW0hr8LteaL JZ5qQ6luFWC2lm+bHvFYTGAGSma6aLZW+msvaARXvIZZ7Ef/0kCmYSq4DxuWhs7MvqOBXV5dViKLl ByVJIKFw==; Received: from [192.168.2.1] (port=45846 helo=steel) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.95) (envelope-from ) id 1mvco1-0002oM-H4; Fri, 10 Dec 2021 15:37:09 +0530 From: Arun Isaac To: Ludovic =?utf-8?Q?Court=C3=A8s?= Subject: Re: bug#52091: [PATCH] gnu: Add ccwl. In-Reply-To: <87fsr1g5ip.fsf_-_@gnu.org> References: <20211129154827.18303-1-arunisaac@systemreboot.net> <20211129154827.18303-2-arunisaac@systemreboot.net> <87fsr1g5ip.fsf_-_@gnu.org> Date: Fri, 10 Dec 2021 15:37:04 +0530 Message-ID: <87czm4hiyf.fsf@systemreboot.net> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 52091-done Cc: 52091-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) --=-=-= Content-Type: text/plain Pushed after adding bash-minimal to inputs (now required due to the wrap-program phase), thank you! --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQFPBAEBCAA5FiEEf3MDQ/Lwnzx3v3nTLiXui2GAK7MFAmGzJsgbHGFydW5pc2Fh Y0BzeXN0ZW1yZWJvb3QubmV0AAoJEC4l7othgCuzsFgH/0pAOVm80sIPhfUVAU1n agWh3i9jFoVf0NehlCkGUtf/AYgFtNgAEKiJPmomh+V8dlLImO2l4sNQY4Dv0c0a YeACCo/egjYuriES9XA56VRpEyKh0xCKbaCth2HAJvXFTZEDrkcUhpjLGZcJYd1g SVxJTJpmUje10djqBFNK8qnm8gpSZ8xULqumhB9oTJwAowa8SAo+WbLkW6w+1ir1 gL/xaPhTA1cJSQVSkdhyDFDMnsTU/9QUs6O6niuCiKjWhzGlmDp9D8D09D4AhBma +usoVZhEpijRCT16Mos6v8neAIbTgxUSjVRbJRFwizR+XJH6NH8eSGvcZZrHMVcI m5Y= =RgKH -----END PGP SIGNATURE----- --=-=-=-- ------------=_1639130882-30581-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit 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 To: guix-patches@gnu.org Subject: [PATCH] gnu: Add ccwl. 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 Content-Transfer-Encoding: 8bit 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-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit Cc: Arun Isaac X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.4 (--) * 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+))) -- 2.34.0 ------------=_1639130882-30581-1--