From patchwork Fri Apr 21 08:16:36 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 49342 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 EECC827BBEA; Fri, 21 Apr 2023 09:18:13 +0100 (BST) 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=ham 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 A7FA027BBE9 for ; Fri, 21 Apr 2023 09:18:12 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pply2-00012i-Rt; Fri, 21 Apr 2023 04:18:06 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pplxz-00011t-SC for guix-patches@gnu.org; Fri, 21 Apr 2023 04:18:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pplxz-00067X-Fy for guix-patches@gnu.org; Fri, 21 Apr 2023 04:18:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pplxz-0000Lt-8r for guix-patches@gnu.org; Fri, 21 Apr 2023 04:18:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62978] [PATCH v2 1/6] gnu: bpp-core: Update to 2.4.1. 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[source]: Remove the commit and use the release version. Changed to the github stored sources. [arguments]: Remove the disabled parallel-build. [home-page]: Changed to new host Université Claude-Bernard Lyon 1. --- gnu/packages/bioinformatics.scm | 42 ++++++++++++++------------------- 1 file changed, 18 insertions(+), 24 deletions(-) base-commit: 904b77e1814b611c256ecf161aa36f58d0882380 diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b27e12a5b4..351387fb06 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2220,34 +2220,28 @@ (define-public qtltools (license license:gpl3+))) (define-public bpp-core - ;; The last release was in 2014 and the recommended way to install from source - ;; is to clone the git repository, so we do this. - ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page - (let ((commit "7d8bced0d1a87291ea8dd7046b7fb5ff9c35c582")) - (package - (name "bpp-core") - (version (string-append "2.2.0-1." (string-take commit 7))) - (source (origin - (method git-fetch) - (uri (git-reference - (url "http://biopp.univ-montp2.fr/git/bpp-core") - (commit commit))) - (file-name (string-append name "-" version "-checkout")) - (sha256 - (base32 - "10djsq5vlnkilv436gnmh4irpk49v29pa69r6xiryg32xmvn909j")))) - (build-system cmake-build-system) - (arguments - `(#:parallel-build? #f)) - (home-page "http://biopp.univ-montp2.fr") - (synopsis "C++ libraries for Bioinformatics") - (description - "Bio++ is a set of C++ libraries for Bioinformatics, including sequence + (package + (name "bpp-core") + (version "2.4.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BioPP/bpp-core") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0ma2cl677l7s0n5sffh66cy9lxp5wycm50f121g8rx85p95vkgwv")))) + (build-system cmake-build-system) + (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-core/html/index.html") + (synopsis "C++ libraries for Bioinformatics") + (description + "Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. It is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.") - (license license:cecill-c)))) + (license license:cecill-c))) (define-public bpp-phyl ;; The last release was in 2014 and the recommended way to install from source From patchwork Fri Apr 21 08:16:37 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 49343 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 853EF27BBEA; Fri, 21 Apr 2023 09:18:33 +0100 (BST) 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=ham 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 7E81E27BBE2 for ; Fri, 21 Apr 2023 09:18:32 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pply1-00012D-H9; Fri, 21 Apr 2023 04:18:05 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pplxz-00011e-2p for guix-patches@gnu.org; Fri, 21 Apr 2023 04:18:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pplxy-00067L-RB for guix-patches@gnu.org; Fri, 21 Apr 2023 04:18:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pplxy-0000Le-G0 for guix-patches@gnu.org; Fri, 21 Apr 2023 04:18:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62978] [PATCH v2 2/6] gnu: bpp-seq: Update to 2.4.1. 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[source]: Remove the commit and use the release version. Changed to the github repo. [arguments]: Remove the disabled parallel-build and out-of-source. [home-page]: Changed to new host Université Claude-Bernard Lyon 1. --- gnu/packages/bioinformatics.scm | 48 +++++++++++++-------------------- 1 file changed, 19 insertions(+), 29 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 351387fb06..232d0e42c6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2308,37 +2308,27 @@ (define-public bpp-popgen (license license:cecill-c)))) (define-public bpp-seq - ;; The last release was in 2014 and the recommended way to install from source - ;; is to clone the git repository, so we do this. - ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page - (let ((commit "6cfa07965ce152e5598a89df2fa80a75973bfa33")) - (package - (name "bpp-seq") - (version (string-append "2.2.0-1." (string-take commit 7))) - (source (origin - (method git-fetch) - (uri (git-reference - (url "http://biopp.univ-montp2.fr/git/bpp-seq") - (commit commit))) - (file-name (string-append name "-" version "-checkout")) - (sha256 - (base32 - "1nys5jq7jqvdg40d91wsmj3q2yzy4276cp7sp44n67p468f27zf2")))) - (build-system cmake-build-system) - (arguments - `(#:parallel-build? #f - ;; If out-of-source, test data is not copied into the build directory - ;; so the tests fail. - #:out-of-source? #f)) - (inputs - (list bpp-core)) - (home-page "http://biopp.univ-montp2.fr") - (synopsis "Bio++ sequence library") - (description - "Bio++ is a set of C++ libraries for Bioinformatics, including sequence + (package + (name "bpp-seq") + (version "2.4.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BioPP/bpp-seq") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1mc09g8jswzsa4wgrfv59jxn15ys3q8s0227p1j838wkphlwn2qk")))) + (build-system cmake-build-system) + (inputs + (list bpp-core)) + (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-seq/html/") + (synopsis "Bio++ sequence library") + (description + "Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. This library provides sequence-related modules.") - (license license:cecill-c)))) + (license license:cecill-c))) (define-public bppsuite ;; The last release was in 2014 and the recommended way to install from source From patchwork Fri Apr 21 08:16:38 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 49345 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 097B127BBE2; Fri, 21 Apr 2023 09:18:45 +0100 (BST) 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=ham 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 2BB9727BBE9 for ; Fri, 21 Apr 2023 09:18:42 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pply6-000149-OZ; Fri, 21 Apr 2023 04:18:10 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pplxy-00011c-BQ for guix-patches@gnu.org; Fri, 21 Apr 2023 04:18:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pplxy-00067G-3Y for guix-patches@gnu.org; Fri, 21 Apr 2023 04:18:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pplxx-0000LX-VP for guix-patches@gnu.org; Fri, 21 Apr 2023 04:18:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62978] [PATCH v2 3/6] gnu: bpp-phyl: Update to 2.4.1. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 Apr 2023 08:18:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 62978 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <62978@debbugs.gnu.org> Received: via spool by 62978-submit@debbugs.gnu.org id=B62978.16820650301215 (code B ref 62978); Fri, 21 Apr 2023 08:18:01 +0000 Received: (at 62978) by debbugs.gnu.org; 21 Apr 2023 08:17:10 +0000 Received: from localhost ([127.0.0.1]:39194 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pplx7-0000JP-E0 for submit@debbugs.gnu.org; Fri, 21 Apr 2023 04:17:10 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:35539) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pplx4-0000If-V4 for 62978@debbugs.gnu.org; Fri, 21 Apr 2023 04:17:08 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1682065020; x=1683879421; bh=O+YWMqfBFARC9QzXu6T09s0eBmaYFgYsx1LoSacIc3w=; b=Hc7zYEBprRh1 QdRrTPQPDenHU6YD9d/UUNbrnfNeGtH/nRkhYjwRtUGRvnPUlQ/94+xKVSy71YVT fp7A5ZYClA6nOWnG01nkQL5gPan0Mg7J+7pan1BASGyHafaPQVkZf0utfAIRdzG0 UTBd7m9icPgzmYy80gxGokCkI4n8x9g= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=madalinionel.patrascu@mdc-berlin.de; receiver= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id C799C160141 for <62978@debbugs.gnu.org>; Fri, 21 Apr 2023 10:17:00 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.23; Fri, 21 Apr 2023 10:16:58 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Fri, 21 Apr 2023 10:16:38 +0200 Message-ID: <20230421081641.18388-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230421081641.18388-1-madalinionel.patrascu@mdc-berlin.de> References: <20230421081641.18388-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27578.006 X-TM-AS-Result: No-10--5.564100-5.000000 X-TMASE-MatchedRID: LfY4/T2Qrh/BP9kF6SLh5hIRh9wkXSlFyiKgKtIyB4qAI7Mvq/sL54PN dYXFrfiyIVOe0TAdekipgf1jMun5ewV2NKF6aideEXjPIvKd74BMkOX0Uoduuc3wMjzgVvguChb 10lmaN/ZYzJcD0gVKSpzSLZJ1HkA9mv0Xhs8HK808o3fwIs8rQX607foZgOWypjlkbDvDJ4dU82 kILwgVLQ1RxwBNHJ3UnAr+uwKiSZbQ3sOMB3Fk1OfOVcxjDhcwoWiH8jJBtC9t1O49r1VEa8RB0 bsfrpPI34T9cYMsdwxlw1+kksNi1xig1GHpIltzNpxF/kaxhUuCafs8/ebTsnYolVCCbqPjC0xk JCsSnHEDNhOBWiZV0QpZ2cS7c3t105U5xoSm3kPcUke23u350xU7OJY7bdPeD9iv/sJMsVc7Oyi /ulxQeKUgZdIaXg4f X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.564100-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27578.006 X-TM-SNTS-SMTP: 4C234F68A75FF268FB41EE488A505E8784EFA51527F47E7786DC9783BA057D5C2002:F 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (bpp-phyl): Update to 2.4.1. [source]: Remove the commit and use the release version. Changed to the github repo. [arguments]: Remove the disabled parallel-build and out-of-source. [home-page]: Changed to new host Université Claude-Bernard Lyon 1. [synopsis]: Use proper capitalization. --- gnu/packages/bioinformatics.scm | 49 ++++++++++++++------------------- 1 file changed, 20 insertions(+), 29 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 232d0e42c6..ad61b979dd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2244,37 +2244,28 @@ (define-public bpp-core (license license:cecill-c))) (define-public bpp-phyl - ;; The last release was in 2014 and the recommended way to install from source - ;; is to clone the git repository, so we do this. - ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page - (let ((commit "0c07167b629f68b569bf274d1ad0c4af83276ae2")) - (package - (name "bpp-phyl") - (version (string-append "2.2.0-1." (string-take commit 7))) - (source (origin - (method git-fetch) - (uri (git-reference - (url "http://biopp.univ-montp2.fr/git/bpp-phyl") - (commit commit))) - (file-name (string-append name "-" version "-checkout")) - (sha256 - (base32 - "1ssjgchzwj3iai26kyly7gwkdv8sk59nqhkb1wpap3sf5m6kyllh")))) - (build-system cmake-build-system) - (arguments - `(#:parallel-build? #f - ;; If out-of-source, test data is not copied into the build directory - ;; so the tests fail. - #:out-of-source? #f)) - (inputs - (list bpp-core bpp-seq)) - (home-page "http://biopp.univ-montp2.fr") - (synopsis "Bio++ phylogenetic Library") - (description - "Bio++ is a set of C++ libraries for Bioinformatics, including sequence + (package + (name "bpp-phyl") + (version "2.4.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BioPP/bpp-phyl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "192zks6wyk903n06c2lbsscdhkjnfwms8p7jblsmk3lvjhdipb20")))) + (build-system cmake-build-system) + (inputs + (list bpp-core bpp-seq)) + (home-page "https://pbil.univ-lyon1.fr/bpp-doc/bpp-phyl/html/") + (synopsis "Bio++ phylogenetic library") + (description + "Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. This library provides phylogenetics-related modules.") - (license license:cecill-c)))) + (license license:cecill-c))) (define-public bpp-popgen ;; The last release was in 2014 and the recommended way to install from source From patchwork Fri Apr 21 08:16:39 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 49346 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 6F71A27BBEA; Fri, 21 Apr 2023 09:18:53 +0100 (BST) 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=ham 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 A7C0327BBE9 for ; Fri, 21 Apr 2023 09:18:52 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pply3-000139-Ll; Fri, 21 Apr 2023 04:18:07 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pplxz-00011s-RK for guix-patches@gnu.org; Fri, 21 Apr 2023 04:18:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pplxz-00067Q-1O for guix-patches@gnu.org; Fri, 21 Apr 2023 04:18:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pplxy-0000Lm-TU for guix-patches@gnu.org; Fri, 21 Apr 2023 04:18:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62978] [PATCH v2 4/6] gnu: Add bpp-seq-omics. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 Apr 2023 08:18:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 62978 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <62978@debbugs.gnu.org> Received: via spool by 62978-submit@debbugs.gnu.org id=B62978.16820650311230 (code B ref 62978); Fri, 21 Apr 2023 08:18:02 +0000 Received: (at 62978) by debbugs.gnu.org; 21 Apr 2023 08:17:11 +0000 Received: from localhost ([127.0.0.1]:39198 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pplx9-0000Jg-Cb for submit@debbugs.gnu.org; Fri, 21 Apr 2023 04:17:11 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:58113) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pplx3-0000IS-Ua for 62978@debbugs.gnu.org; Fri, 21 Apr 2023 04:17:08 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1682065019; x=1683879420; bh=NCUiKHryk2DNnOICLb35T6HjW/AbH4Wj8/F54A0cpXA=; b=hbKYOUYYU26l lLD8Kr7n8NudNEp8/R/3NedvY9JYnKwOsntsKgsfCd4D9zBMKCE2X1IruJCotNlu 1yZgWJzKPg5VleY+7AfpgtJ7FWDscR/O2XNnCtlnfLiHdu8R7XqAPrUyKZ01Bb7N nhY+qAPaHrunQ0iCOWFqGYxx+xMFtXk= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=madalinionel.patrascu@mdc-berlin.de; receiver= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 57640160123 for <62978@debbugs.gnu.org>; Fri, 21 Apr 2023 10:16:59 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.23; Fri, 21 Apr 2023 10:16:58 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Fri, 21 Apr 2023 10:16:39 +0200 Message-ID: <20230421081641.18388-4-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230421081641.18388-1-madalinionel.patrascu@mdc-berlin.de> References: <20230421081641.18388-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27578.006 X-TM-AS-Result: No-10--5.088400-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcN6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VNnf JrUSEbFD5U2NzhfTq9zuNT8xdcEnQwE+dA3RWUSvnVTWWiNp+v/KIqAq0jIHisHBVqFYzBaDYxa 8wxTbhnt7MSP7SLpuGAoRYADvfikpuJXEeLLJ6+yrm7DrUlmNkIAy6p60ZV62yA7duzCw6dLdB/ CxWTRRu92KvEVWmYr1DDn84cLDHIcuw/s6ASVJxirhCkiRKlmAn6Aq7aJDNCBD3MczAU0odw== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.088400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27578.006 X-TM-SNTS-SMTP: 7773E230099C5F8C54A63A1CE8AAA777B40A5E3CF4F5386CF19DDCC8C60DE6DD2002:F 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (bpp-seq-omics): New variable. --- gnu/packages/bioinformatics.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ad61b979dd..576af31ae6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2321,6 +2321,28 @@ (define-public bpp-seq library provides sequence-related modules.") (license license:cecill-c))) +(define-public bpp-seq-omics + (package + (name "bpp-seq-omics") + (version "2.4.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BioPP/bpp-seq-omics") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1sc2xdfnfp5a6qihplp49rgrqmj89898avfy9bqaq1g2fajppgjj")))) + (build-system cmake-build-system) + (inputs + (list bpp-core bpp-seq)) + (home-page "https://github.com/BioPP/bpp-seq-omics") + (synopsis "Bio++ sequence library genomics components") + (description + "This library contains the genomics components of the Bio++ sequence library. +It is part of the Bio++ project.") + (license license:cecill))) + (define-public bppsuite ;; The last release was in 2014 and the recommended way to install from source ;; is to clone the git repository, so we do this. From patchwork Fri Apr 21 08:16:40 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 49347 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 E32BE27BBE9; Fri, 21 Apr 2023 09:18:55 +0100 (BST) 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=ham 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 36A3F27BBEA for ; Fri, 21 Apr 2023 09:18:55 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pply3-00012k-2t; Fri, 21 Apr 2023 04:18:07 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pply1-00012T-OQ for guix-patches@gnu.org; Fri, 21 Apr 2023 04:18:05 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pplxz-00067i-Th for guix-patches@gnu.org; Fri, 21 Apr 2023 04:18:05 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pplxz-0000M1-PO for guix-patches@gnu.org; Fri, 21 Apr 2023 04:18:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62978] [PATCH v2 5/6] gnu: Add bpp-phyl-omics. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 Apr 2023 08:18:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 62978 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <62978@debbugs.gnu.org> Received: via spool by 62978-submit@debbugs.gnu.org id=B62978.16820650401263 (code B ref 62978); Fri, 21 Apr 2023 08:18:03 +0000 Received: (at 62978) by debbugs.gnu.org; 21 Apr 2023 08:17:20 +0000 Received: from localhost ([127.0.0.1]:39204 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pplxI-0000KI-5e for submit@debbugs.gnu.org; Fri, 21 Apr 2023 04:17:20 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:50285) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pplx6-0000It-1w for 62978@debbugs.gnu.org; Fri, 21 Apr 2023 04:17:10 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1682065022; x=1683879423; bh=WG7RJg04W96Mg7I2fyiixgXCokVI++IXWdVhw1wHOR8=; b=oNi4YHTgTRzS QUl44nQmxgZy2hSnifxaIXcgjS/LOlkZdy95fk/CXROnXYBQevmvvwVOOZ3MnHIP enNGJGJqhYUIxrOSKuqbstZs/FDF43XOynVXjEYDnFSydC8Y2rpHRKPMVHabqE82 jaPXlTQCLV+9IfawCAxsZOtDxWQN3UE= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=madalinionel.patrascu@mdc-berlin.de; receiver= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id F184616014E for <62978@debbugs.gnu.org>; Fri, 21 Apr 2023 10:17:01 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.23; Fri, 21 Apr 2023 10:16:58 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Fri, 21 Apr 2023 10:16:40 +0200 Message-ID: <20230421081641.18388-5-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230421081641.18388-1-madalinionel.patrascu@mdc-berlin.de> References: <20230421081641.18388-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27578.006 X-TM-AS-Result: No-10--7.601400-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfN6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VNnf JrUSEbFD5U2NzhfTq9zuNT8xdcEnQwE+dA3RWUSvnVTWWiNp+v/KIqAq0jIHihPiIPO2d8g5Uex gNDoxdJZ67OLuIAmsavAZSzjX62drJnckDi37jO7TfU1/F+PbM2yiYnmnxjh8U72YOAMDJjieAi CmPx4NwBnUJ0Ek6yhjxEHRux+uk8hfNjF5BHUO+zILdKULpe6ayMq2D6cFuEhqaIzZRKSQtVVoH SPuzHq4SS/2ITVqjcI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.601400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27578.006 X-TM-SNTS-SMTP: 02E44AE5C08AC59476F0EF7597B3FAF8119BD14228629B15AD23A423626F49842002:F 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (bpp-phyl-omics): New variable. --- gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 576af31ae6..511431fb95 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2267,6 +2267,34 @@ (define-public bpp-phyl library provides phylogenetics-related modules.") (license license:cecill-c))) +(define-public bpp-phyl-omics + (package + (name "bpp-phyl-omics") + (version "2.4.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BioPP/bpp-phyl-omics") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "172psb8njkjwg3cd6gdy5w0mq8f0817v635yw4bk7146aggjzl1h")))) + (build-system cmake-build-system) + (arguments + (list #:tests? #f)) ; No test provided. + (inputs + (list bpp-core + bpp-phyl + bpp-seq + bpp-seq-omics)) + (home-page "https://github.com/BioPP/bpp-phyl-omics") + (synopsis "Bio++ phylogenetic library genomics components") + (description + "This library contains the genomics components of the Bio++ phylogenetics +library. It is part of the Bio++ project.") + (license license:cecill))) + (define-public bpp-popgen ;; The last release was in 2014 and the recommended way to install from source ;; is to clone the git repository, so we do this. From patchwork Fri Apr 21 08:16:41 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 49344 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 D168E27BBEC; Fri, 21 Apr 2023 09:18:42 +0100 (BST) 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=ham 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 18C8C27BBE2 for ; Fri, 21 Apr 2023 09:18:42 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pply3-00012u-Iq; Fri, 21 Apr 2023 04:18:07 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pply2-00012S-08 for guix-patches@gnu.org; Fri, 21 Apr 2023 04:18:06 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pply0-00067j-A2 for guix-patches@gnu.org; Fri, 21 Apr 2023 04:18:05 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pply0-0000M8-6W for guix-patches@gnu.org; Fri, 21 Apr 2023 04:18:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62978] [PATCH v2 6/6] gnu: Add maffilter. 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(license license:bsd-3))) +(define-public maffilter + (package + (name "maffilter") + (version "1.3.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/jydu/maffilter/archive/v" + version ".tar.gz")) + (sha256 + (base32 "0xgbadjad54hjdh743qszyv4yvdpi45519h6cj6sfgybsr93385l")))) + (build-system cmake-build-system) + (arguments + (list #:tests? #f)) ; No tests provided. + (inputs + (list bpp-core + bpp-phyl + bpp-phyl-omics + bpp-seq + bpp-seq-omics + boost + zlib)) + (home-page "https://jydu.github.io/maffilter/") + (synopsis "Multiple alignment format file processor") + (description + "MafFilter is a program dedicated to the analysis of genome alignments. It +parses and manipulates @acronym{MAF, multiple alignment format} files as well as +more simple fasta files. This package can be used to design a pipeline as a +series of consecutive filters, each performing a dedicated analysis. Many of +the filters are available, from alignment cleaning to phylogeny reconstruction +and population genetics analysis. Despite various filtering options and format +conversion tools, MafFilter can compute a wide range of statistics (phylogenetic +trees, nucleotide diversity, inferrence of selection, etc.).") + (license license:gpl3))) + (define-public mafft (package (name "mafft")