From unknown Wed Jun 18 23:11:28 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#29017 <29017@debbugs.gnu.org> To: bug#29017 <29017@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Add gwl. Reply-To: bug#29017 <29017@debbugs.gnu.org> Date: Thu, 19 Jun 2025 06:11:28 +0000 retitle 29017 [PATCH] gnu: Add gwl. reassign 29017 guix-patches submitter 29017 Roel Janssen severity 29017 normal tag 29017 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Thu Oct 26 16:51:36 2017 Received: (at submit) by debbugs.gnu.org; 26 Oct 2017 20:51:36 +0000 Received: from localhost ([127.0.0.1]:35544 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e7p7n-000711-Or for submit@debbugs.gnu.org; Thu, 26 Oct 2017 16:51:36 -0400 Received: from eggs.gnu.org ([208.118.235.92]:56991) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e7p7l-00070o-V7 for submit@debbugs.gnu.org; Thu, 26 Oct 2017 16:51:34 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1e7p7f-0001xr-8w for submit@debbugs.gnu.org; Thu, 26 Oct 2017 16:51:28 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-0.0 required=5.0 tests=BAYES_20,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:32792) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1e7p7f-0001xg-4h for submit@debbugs.gnu.org; Thu, 26 Oct 2017 16:51:27 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:47944) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1e7p7d-0003KI-LX for guix-patches@gnu.org; Thu, 26 Oct 2017 16:51:26 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1e7p7Z-0001sc-DR for guix-patches@gnu.org; Thu, 26 Oct 2017 16:51:25 -0400 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:34757) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1e7p7Z-0001sQ-8I for guix-patches@gnu.org; Thu, 26 Oct 2017 16:51:21 -0400 Received: from ip112-245-209-87.adsl2.static.versatel.nl ([87.209.245.112]:64468 helo=yellowstone) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1e7p7Y-0001PH-RI for guix-patches@gnu.org; Thu, 26 Oct 2017 16:51:21 -0400 User-agent: mu4e 0.9.18; emacs 25.1.1 From: Roel Janssen To: guix-patches Subject: [PATCH] gnu: Add gwl. Date: Thu, 26 Oct 2017 22:51:12 +0200 Message-ID: <87h8ulhbun.fsf@gnu.org> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: submit 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: -5.0 (-----) --=-=-= Content-Type: text/plain Dear Guix, I would like to add GWL. For a lack of a better place, I chose the bioinformatics module because that's where we use this package. Thanks for your time! Kind regards, Roel Janssen --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0001-gnu-Add-gwl.patch >From eaa22755769973ba30600ae96bb92a5d6bad11dd Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 26 Oct 2017 22:46:50 +0200 Subject: [PATCH] gnu: Add gwl. * gnu/packages/bioinformatics.scm (gwl): New variable. --- gnu/packages/bioinformatics.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 43a00f196..ac7320040 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -70,6 +70,7 @@ #:use-module (gnu packages java) #:use-module (gnu packages ldc) #:use-module (gnu packages linux) + #:use-module (gnu packages lisp) #:use-module (gnu packages logging) #:use-module (gnu packages machine-learning) #:use-module (gnu packages man) @@ -77,6 +78,7 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages ncurses) #:use-module (gnu packages ocaml) + #:use-module (gnu packages package-management) #:use-module (gnu packages pcre) #:use-module (gnu packages parallel) #:use-module (gnu packages pdf) @@ -9755,6 +9757,37 @@ knowledge of gene annotation information. GESS stands for the graph-based exon-skipping scanner detection scheme.") (license license:bsd-3))) +(define-public gwl + (package + (name "gwl") + (version "0.1.0") + (source (origin + (method url-fetch) + (uri (string-append "https://git.roelj.com/attachments/" + "d804e310-b9c0-44b1-bd18-c7505e9f9d9b")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1x4swwp7kmhd57j3scii5c4h8swkcvab2r6mz7wxwwbx300wcqpy")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("pkg-config" ,pkg-config))) + (inputs + `(("guix" ,guix) + ("guile" ,guile-2.2) + ("guile-commonmark" ,guile-commonmark))) + (home-page "https://www.guixwl.org") + (synopsis "Workflow management extension for GNU Guix") + (description "This project provides two subcommands to GNU Guix and +introduces two record types that provide a workflow management extension built +on top of GNU Guix.") + ;; The Scheme modules in guix/ and gnu/ are licensed GPL3+, + ;; the web interface modules in gwl/ are licensed AGPL3+, + ;; and the fonts included in this package are licensed OFL1.1. + (license (list license:gpl3+ license:agpl3+ license:silofl1.1)))) + (define-public phylip (package (name "phylip") -- 2.14.2 --=-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Thu Oct 26 18:41:50 2017 Received: (at 29017) by debbugs.gnu.org; 26 Oct 2017 22:41:50 +0000 Received: from localhost ([127.0.0.1]:35700 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e7qqU-0001J9-Cp for submit@debbugs.gnu.org; Thu, 26 Oct 2017 18:41:50 -0400 Received: from hera.aquilenet.fr ([141.255.128.1]:53262) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e7qqS-0001J1-Il for 29017@debbugs.gnu.org; Thu, 26 Oct 2017 18:41:49 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 7A48EF51A; Fri, 27 Oct 2017 00:41:48 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id vJPX71QCTPmG; Fri, 27 Oct 2017 00:41:47 +0200 (CEST) Received: from ribbon (unknown [72.28.92.23]) by hera.aquilenet.fr (Postfix) with ESMTPSA id CB47D8B30; Fri, 27 Oct 2017 00:41:46 +0200 (CEST) From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Roel Janssen Subject: Re: [bug#29017] [PATCH] gnu: Add gwl. References: <87h8ulhbun.fsf@gnu.org> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 5 Brumaire an 226 de la =?utf-8?Q?R=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-pc-linux-gnu Date: Thu, 26 Oct 2017 15:41:42 -0700 In-Reply-To: <87h8ulhbun.fsf@gnu.org> (Roel Janssen's message of "Thu, 26 Oct 2017 22:51:12 +0200") Message-ID: <87wp3hcz15.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 29017 Cc: 29017@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 (+) Hello! Roel Janssen skribis: > I would like to add GWL. For a lack of a better place, I chose the > bioinformatics module because that's where we use this package. Awesome! \o/ Perhaps that could go to package-management.scm? > From eaa22755769973ba30600ae96bb92a5d6bad11dd Mon Sep 17 00:00:00 2001 > From: Roel Janssen > Date: Thu, 26 Oct 2017 22:46:50 +0200 > Subject: [PATCH] gnu: Add gwl. > > * gnu/packages/bioinformatics.scm (gwl): New variable. [...] > +(define-public gwl > + (package > + (name "gwl") > + (version "0.1.0") > + (source (origin > + (method url-fetch) > + (uri (string-append "https://git.roelj.com/attachments/" > + "d804e310-b9c0-44b1-bd18-c7505e9f9d9b"= )) Do you have a more =E2=80=9Cstandard=E2=80=9D URL, such as a cgit snapshot?= If not that=E2=80=99s fine. > + (inputs > + `(("guix" ,guix) > + ("guile" ,guile-2.2) > + ("guile-commonmark" ,guile-commonmark))) It might be that you either need to propagate Guix and CommonMark, or to wrap the binaries that GWL provides (as is done in the =E2=80=98guix=E2=80= =99 package), no? Otherwise LGTM, thank you! Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Fri Oct 27 07:26:45 2017 Received: (at 29017) by debbugs.gnu.org; 27 Oct 2017 11:26:45 +0000 Received: from localhost ([127.0.0.1]:35990 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e82mj-0000K6-J4 for submit@debbugs.gnu.org; Fri, 27 Oct 2017 07:26:45 -0400 Received: from eggs.gnu.org ([208.118.235.92]:51538) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e82mh-0000Js-J1 for 29017@debbugs.gnu.org; Fri, 27 Oct 2017 07:26:44 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1e82mb-0003Ip-CZ for 29017@debbugs.gnu.org; Fri, 27 Oct 2017 07:26:38 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:52769) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1e82mV-0003Fn-I6; Fri, 27 Oct 2017 07:26:31 -0400 Received: from ip-80-113-14-101.ip.prioritytelecom.net ([80.113.14.101]:58091 helo=yellowstone) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1e82mV-0005sr-1D; Fri, 27 Oct 2017 07:26:31 -0400 References: <87h8ulhbun.fsf@gnu.org> <87wp3hcz15.fsf@gnu.org> User-agent: mu4e 0.9.18; emacs 25.1.1 From: Roel Janssen To: Ludovic =?utf-8?Q?Court=C3=A8s?= Subject: Re: [bug#29017] [PATCH] gnu: Add gwl. Message-ID: <87fua4estm.fsf@gnu.org> In-reply-to: <87wp3hcz15.fsf@gnu.org> Date: Fri, 27 Oct 2017 13:26:24 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 29017 Cc: 29017@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: -5.0 (-----) Ludovic Courtès writes: > Hello! > > Roel Janssen skribis: > >> I would like to add GWL. For a lack of a better place, I chose the >> bioinformatics module because that's where we use this package. > > Awesome! \o/ > > Perhaps that could go to package-management.scm? The new patch adds it to package-management.scm. > >> From eaa22755769973ba30600ae96bb92a5d6bad11dd Mon Sep 17 00:00:00 2001 >> From: Roel Janssen >> Date: Thu, 26 Oct 2017 22:46:50 +0200 >> Subject: [PATCH] gnu: Add gwl. >> >> * gnu/packages/bioinformatics.scm (gwl): New variable. > > [...] > >> +(define-public gwl >> + (package >> + (name "gwl") >> + (version "0.1.0") >> + (source (origin >> + (method url-fetch) >> + (uri (string-append "https://git.roelj.com/attachments/" >> + "d804e310-b9c0-44b1-bd18-c7505e9f9d9b")) > > Do you have a more “standard” URL, such as a cgit snapshot? If not > that’s fine. This I found a bit weird about Gogs. Custom-uploaded tarballs get these weird URLs. I uploaded the same tarball to guixwl.org, and adjusted the recipe to use that URL. > >> + (inputs >> + `(("guix" ,guix) >> + ("guile" ,guile-2.2) >> + ("guile-commonmark" ,guile-commonmark))) > > It might be that you either need to propagate Guix and CommonMark, or to > wrap the binaries that GWL provides (as is done in the ‘guix’ package), > no? I added guix and guile-commonmark to the propagated-inputs. > > Otherwise LGTM, thank you! > > Ludo’. Thanks for your quick response! I pushed the new patch in 58a308e0b. Kind regards, Roel Janssen From debbugs-submit-bounces@debbugs.gnu.org Fri Oct 27 10:08:47 2017 Received: (at 29017-done) by debbugs.gnu.org; 27 Oct 2017 14:08:48 +0000 Received: from localhost ([127.0.0.1]:37461 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e85JX-0001tr-Op for submit@debbugs.gnu.org; Fri, 27 Oct 2017 10:08:47 -0400 Received: from eggs.gnu.org ([208.118.235.92]:39547) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e85JV-0001tf-Ks for 29017-done@debbugs.gnu.org; Fri, 27 Oct 2017 10:08:45 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1e85JP-0005HO-V1 for 29017-done@debbugs.gnu.org; Fri, 27 Oct 2017 10:08:40 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:58101) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1e85JK-0005FH-Pk; Fri, 27 Oct 2017 10:08:34 -0400 Received: from ip-80-113-14-101.ip.prioritytelecom.net ([80.113.14.101]:52831 helo=yellowstone) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1e85JK-0005Md-Bi; Fri, 27 Oct 2017 10:08:34 -0400 References: <87h8ulhbun.fsf@gnu.org> <87wp3hcz15.fsf@gnu.org> <87fua4estm.fsf@gnu.org> User-agent: mu4e 0.9.18; emacs 25.1.1 From: Roel Janssen To: Ludovic =?utf-8?Q?Court=C3=A8s?= Subject: Re: [bug#29017] [PATCH] gnu: Add gwl. In-reply-to: <87fua4estm.fsf@gnu.org> Date: Fri, 27 Oct 2017 16:08:26 +0200 Message-ID: <87po98n0o5.fsf@gnu.org> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 29017-done Cc: 29017-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: -5.0 (-----) From unknown Wed Jun 18 23:11:28 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. 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