From unknown Sat Sep 20 13:26:29 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#62978 <62978@debbugs.gnu.org> To: bug#62978 <62978@debbugs.gnu.org> Subject: Status: gnu: bpp-core, bpp-seq, bpp-phyl: Update to 2.4.1. && gnu: Add bpp-seq-omics, bpp-phyl-omics and maffilter. Reply-To: bug#62978 <62978@debbugs.gnu.org> Date: Sat, 20 Sep 2025 20:26:29 +0000 retitle 62978 gnu: bpp-core, bpp-seq, bpp-phyl: Update to 2.4.1. && gnu: A= dd bpp-seq-omics, bpp-phyl-omics and maffilter. reassign 62978 guix-patches submitter 62978 "MadalinIonel.Patrascu@mdc-berlin.de" severity 62978 normal thanks From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 20 19:02:34 2023 Received: (at submit) by debbugs.gnu.org; 20 Apr 2023 23:02:34 +0000 Received: from localhost ([127.0.0.1]:38835 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppdIQ-0007f9-DA for submit@debbugs.gnu.org; Thu, 20 Apr 2023 19:02:34 -0400 Received: from lists.gnu.org ([209.51.188.17]:60796) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppdIO-0007f1-11 for submit@debbugs.gnu.org; Thu, 20 Apr 2023 19:02:32 -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 1ppdIN-0003bR-Js for guix-patches@gnu.org; Thu, 20 Apr 2023 19:02:31 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ppdIL-0004IZ-6r for guix-patches@gnu.org; Thu, 20 Apr 2023 19:02:31 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= mime-version:content-type:content-type:content-language :accept-language:message-id:date:date:subject:subject:from:from :received:received; s=mdc; t=1682031736; x=1683846137; bh=xaAtMJ TshyvESjJsaxfA+UIcZr5Q1odBTznPm3Ga31Y=; b=YnphLg/4/cd58uZ89h7g7B 9OqOyq9vpws8Oa+kBVuLaYOly48QmkOfneJC0cP9YG80+jcGAXr/jGDPs44rIsuZ wIqfeIq3Tqq0jkPzzmbvJ+Yxt2/cPeSBC3QeCSPBTjWj9eB5p2NxxxeSNycQHvu1 a1G7gzjpTl3/LwTt/Vm1U= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.54; helo=sw-it-p-ex1.mdc-berlin.net; envelope-from=madalinionel.patrascu@mdc-berlin.de; receiver= Received: from SW-IT-P-EX1.mdc-berlin.net (mgw1.mdc-berlin.de [141.80.113.54]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 54032300195 for ; Fri, 21 Apr 2023 01:02:16 +0200 (CEST) Received: from SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) by SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) 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 01:02:15 +0200 Received: from SW-IT-P-EX4.mdc-berlin.net ([fe80::e55f:895f:3b41:ec6a]) by SW-IT-P-EX4.mdc-berlin.net ([fe80::e55f:895f:3b41:ec6a%2]) with mapi id 15.01.2507.023; Fri, 21 Apr 2023 01:02:15 +0200 From: "MadalinIonel.Patrascu@mdc-berlin.de" To: "guix-patches@gnu.org" Subject: gnu: bpp-core, bpp-seq, bpp-phyl: Update to 2.4.1. && gnu: Add bpp-seq-omics, bpp-phyl-omics and maffilter. Thread-Topic: bpp-core, bpp-seq, bpp-phyl: Update to 2.4.1. && gnu: Add bpp-seq-omics, bpp-phyl-omics and maffilter. 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--_000_35e32a70b3e1436081ae3caf98c11582mdcberlinde_-- From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 20 19:05:53 2023 Received: (at 62978) by debbugs.gnu.org; 20 Apr 2023 23:05:53 +0000 Received: from localhost ([127.0.0.1]:38852 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppdLc-0007l9-A4 for submit@debbugs.gnu.org; Thu, 20 Apr 2023 19:05:53 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:40653) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppdLa-0007ki-S1 for 62978@debbugs.gnu.org; Thu, 20 Apr 2023 19:05:51 -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=1682031943; x=1683846344; bh=j5N+Zf4hl9woJDGEe93v/CQCRKIs9wdQA7iik23afZ4=; b=JOOa+weQD9JN Nr0rMrFu5u951DGEMOIHxbuVJJXivo8imyqOG3mIqU//CXCSEwxiPefVu0wf0xh4 B3HvfuxZt2H/NbWSwy9qXD/EDZSvqQh5mbCnLGgPyb4agC+Vc9VR8dS3/SBn9nSa PayrkPMGYA+TyGma5VSPvgaH/A2YTLg= 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 B002616011B for <62978@debbugs.gnu.org>; Fri, 21 Apr 2023 01:05:43 +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 01:05:42 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62978@debbugs.gnu.org> Subject: Date: Fri, 21 Apr 2023 01:05:20 +0200 Message-ID: <20230420230523.6648-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230420230523.6648-1-madalinionel.patrascu@mdc-berlin.de> References: <20230420230523.6648-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27578.003 X-TM-AS-Result: No-10--1.964500-5.000000 X-TMASE-MatchedRID: /VWSV+o5dfMPK2Dvdm/TZrQJVdi+qYBRC//1TMV5chOTyUSlW9SxOsPW B/sHSqRCD8ATtev9xHB6PBB2sP26Zx/Qfe1gmZY9ag//jiWuh4P1+9bO3CCbk0J1hMCC63pYDMo 0XQZly2gi+t+0AiFaYvL3NxFKQpq1PM9se4/5kCHvVbHa5Rs8t3LhUU/qa4OGYUdWP7oX6sgR+n GwGZoils+R2FghEhkwXR1LGND1TpQmdyQOLfuM7sarbFSPCqya+KgiyLtJrSAlSIYWv45KipgNM iEzDc45fS0Ip2eEHnyuq6cLRWM2k7Ln+0Vm71LcYhkeD3vG8XcLbigRnpKlKTpcQTtiHDgW2KhU oatArM/qjFam1Um+aKzB6ALTB2nt7saTjm7FCtFGK0AEDKa2f9GgsDDZ7lCWLdhAjJBnvaR3037 Pu3WPm3sgLdkmAaT43yJq1ESN+kMTydv0PB1DgLaNtJpvWmDRSPEWnCfndI5+GPkJmSZLIg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.964500-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27578.003 X-TM-SNTS-SMTP: 96C8936962E4DA73A0598682892549C06FFD83E964398B295A15567D185BF5CD2002:F X-Spam-Score: -0.3 (/) X-Debbugs-Envelope-To: 62978 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: -1.3 (-) Date: Thu, 20 Apr 2023 23:59:42 +0200 Subject: [PATCH 3/6] gnu: bpp-phyl: Update to 2.4.1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * 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. --- 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 -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 20 19:05:53 2023 Received: (at 62978) by debbugs.gnu.org; 20 Apr 2023 23:05:53 +0000 Received: from localhost ([127.0.0.1]:38854 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppdLd-0007lQ-4P for submit@debbugs.gnu.org; Thu, 20 Apr 2023 19:05:53 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:39389) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppdLa-0007kl-S2 for 62978@debbugs.gnu.org; Thu, 20 Apr 2023 19:05:51 -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=1682031945; x=1683846346; bh=PMKMq+3SgXNel0MLUGvGfLVAlvq7f2LyJ6uWGtqB4UY=; b=MQw91W0yYHip UYQ0gDKvgjf9YxZP4v6BouclAJ3tQJV/KRlfi5nbtgEGm866EqCTA5QpGbtm8/A/ 4ca2exXW7L5ZZNh6shwXDFV7OW4BN7nsfeF8l74z/ScrOlcPmyIlmBCJLHRnNKb4 7wBuAF7Chkc6h0KLiCF7mcPT7NgEn5s= 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 0708A16013D for <62978@debbugs.gnu.org>; Fri, 21 Apr 2023 01:05:45 +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 01:05:42 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62978@debbugs.gnu.org> Subject: Date: Fri, 21 Apr 2023 01:05:19 +0200 Message-ID: <20230420230523.6648-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230420230523.6648-1-madalinionel.patrascu@mdc-berlin.de> References: <20230420230523.6648-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27578.003 X-TM-AS-Result: No-10--1.964500-5.000000 X-TMASE-MatchedRID: YqNyETunohoPK2Dvdm/TZrQJVdi+qYBRC//1TMV5chOTyUSlW9SxOsPW B/sHSqRCD8ATtev9xHB6PBB2sP26Zx/Qfe1gmZY9ag//jiWuh4P1+9bO3CCbk0J1hMCC63pYDMo 0XQZly2gi+t+0AiFaYvL3NxFKQpq1PM9se4/5kCHvVbHa5Rs8t3LhUU/qa4OGYUdWP7oX6sgR+n GwGZoils+R2FghEhkwXR1LGND1TpQmdyQOLfuM7sarbFSPCqya+KgiyLtJrSAlSIYWv45KipSDl QPoCUXSxfigqRhN+wibKItl61J/ybEGdp24ZQ9wSlnU38LCY8tm8n7jDidmdd0H8LFZNFG7doMs sNsUwYVdw7dRQKmKsw468sUQAIHnXAlf9qFOKkJ/lgjRVrbQeWxCyoprlWZIgJ4MUXddWxzJLaO 12EjCPFLQdNbm6MLzs+gzW7/EvrTHpeHdXLjLb473WzsXAufzELZrsYgA6obyh3JNelCjdRkfAF x3Dn4y X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.964500-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27578.003 X-TM-SNTS-SMTP: 571F709C98E88BEEB1173D5C2097EA76AEA2F8C9454EA56C57C1D8A5DA2BBB032002:F X-Spam-Score: -0.3 (/) X-Debbugs-Envelope-To: 62978 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: -1.3 (-) Date: Thu, 20 Apr 2023 23:48:04 +0200 Subject: [PATCH 2/6] gnu: bpp-seq: Update to 2.4.1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/bioinformatics.scm (bpp-seq): 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. --- 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 -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 20 19:06:05 2023 Received: (at 62978) by debbugs.gnu.org; 20 Apr 2023 23:06:05 +0000 Received: from localhost ([127.0.0.1]:38859 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppdLo-0007mQ-JM for submit@debbugs.gnu.org; Thu, 20 Apr 2023 19:06:05 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:34815) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppdLa-0007kj-Sf for 62978@debbugs.gnu.org; Thu, 20 Apr 2023 19:05:52 -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 :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1682031944; x=1683846345; bh=wvi+qucL4qZjdqN ylnTEPNQY6DQkNIGc5BR5qzukxiI=; b=SW5f8kNjrWn11oV/su+8TyiHblNaRq2 DwH26EsKNzPeQAxVXQF8+wTfwcnOM/1laPk08oWl7ebRCfS8hSkrbj++cuSgSNwh b1Dr4RcMib8nwHpdySWk4xsffXXXofhO4zXa7UP2gyNBLDxNDozB3pbeHuQrXwrp yki5J0trl9XE= 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 7668F160123 for <62978@debbugs.gnu.org>; Fri, 21 Apr 2023 01:05:44 +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 01:05:42 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62978@debbugs.gnu.org> Subject: Date: Fri, 21 Apr 2023 01:05:18 +0200 Message-ID: <20230420230523.6648-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27578.003 X-TM-AS-Result: No-10-2.205500-5.000000 X-TMASE-MatchedRID: HSepP05xqB0PK2Dvdm/TZrQJVdi+qYBRC//1TMV5chOTyUSlW9SxOsPW B/sHSqRCD8ATtev9xHB6PBB2sP26Zx/Qfe1gmZY9Zj7E6vHnuNbF0kjYVlocoVgLks93sG9tvwU evDt+uW5/XjpbSJS7a5BiPSJiPDCdU6k75K+J6PAwo+sXt0rns/Wr7HvOSElavXw8LKjd3Vk0oI W/6XAMMimSf7W38vN9UUu8YxG/ncTaNaqBfjxBEqncG1vVsfbQLBZz7nFdWD6KtcrCRXmud5SDl QPoCUXSF9I3HgybRyFh3TRrr73/KKPFjJEFr+olzlDRp7RQj9ChaIfyMkG0L23U7j2vVURrxEHR ux+uk8jfhP1xgyx3DGMeetUbs2D4BZZroYBhcvqlYxzjYVA0Wx9mJ9Jff4TmYbficF4npHDJHaU 5fpRUBR9O6tPKbVYG4qB1RlNqUZZML5sRJU5vr9xSR7be7fnTFTs4ljtt094P2K/+wkyxVzs7KL +6XFB4pSBl0hpeDh8= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-2.205500-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27578.003 X-TM-SNTS-SMTP: 3D59648F876F3D209F59C72B93319CD158BC42C0DF656A43A242751350EDFF582002:F X-Spam-Score: -0.3 (/) X-Debbugs-Envelope-To: 62978 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: -1.3 (-) Date: Thu, 20 Apr 2023 23:30:44 +0200 Subject: [PATCH 1/6] gnu: bpp-core: Update to 2.4.1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/bioinformatics.scm (bpp-core): Update to 2.4.1. [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(-) 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 base-commit: 2d06dfc050114dba44e791d8decc8eaa705fee01 -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 20 19:06:05 2023 Received: (at 62978) by debbugs.gnu.org; 20 Apr 2023 23:06:05 +0000 Received: from localhost ([127.0.0.1]:38861 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppdLp-0007mS-3O for submit@debbugs.gnu.org; Thu, 20 Apr 2023 19:06:05 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:54871) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppdLb-0007km-8w for 62978@debbugs.gnu.org; Thu, 20 Apr 2023 19:05:52 -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=1682031945; x=1683846346; bh=GHhCwj/aJfCZlta8iYG46aFfXoiYYuX1cLfvz892/Vc=; b=dtSX5mGYiM79 SduoZVxtJ+4TVvNm8E2D2IciitGNJ/4URXYcnDWV3yLof9XAi0zVycoyfV1HNooJ U+p1Qu6EZl7oEcdOlY0A/v7Dr7IQ9NrDM0e8cbpf//Mg4TXZcoRaxH3tqoWQPQLd rNKd5Q1baiQxlXf69/tSPdMCrBXYbgU= 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 7FADE160141 for <62978@debbugs.gnu.org>; Fri, 21 Apr 2023 01:05:45 +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 01:05:42 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62978@debbugs.gnu.org> Subject: Date: Fri, 21 Apr 2023 01:05:21 +0200 Message-ID: <20230420230523.6648-4-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230420230523.6648-1-madalinionel.patrascu@mdc-berlin.de> References: <20230420230523.6648-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27578.003 X-TM-AS-Result: No-10--5.972600-5.000000 X-TMASE-MatchedRID: EQQacRDqAQsPK2Dvdm/TZqoXHZz/dXlxuemKEMcWmztYC5LPd7Bvbb8F Hrw7frluf146W0iUu2uD0fiPNa0yFh1hN+DNBjvOa87CDXaKRVILwteD+QnyUBHfiujuTbedcUL R8x5ADnDpdy8Hf5kviBZi3foHKexSkto8AKCDbo5uq3SU2oCL/hDkv2q7d+VDlwV2iaAfSWf4cK Zpr+0wdhnUJ0Ek6yhjxEHRux+uk8hfNjF5BHUO+zuXoD1F16zGggeuABG95xmYq+TPXpvXT4hqy 3QkNKVwqgg3S9fmf34= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.972600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27578.003 X-TM-SNTS-SMTP: 96EBA729441FF3F655793131E0583FCB133EBB4ED61D76BE230AF0E559507FAA2002:F X-Spam-Score: -0.3 (/) X-Debbugs-Envelope-To: 62978 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: -1.3 (-) Date: Fri, 21 Apr 2023 00:28:46 +0200 Subject: [PATCH 4/6] gnu: Add bpp-seq-omics. * 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. -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 20 19:06:05 2023 Received: (at 62978) by debbugs.gnu.org; 20 Apr 2023 23:06:06 +0000 Received: from localhost ([127.0.0.1]:38863 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppdLp-0007mZ-ED for submit@debbugs.gnu.org; Thu, 20 Apr 2023 19:06:05 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:56059) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppdLb-0007kn-N9 for 62978@debbugs.gnu.org; Thu, 20 Apr 2023 19:05:52 -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=1682031946; x=1683846347; bh=HHaetR6BMPaVXxi5/JCcsaFjlkm19oHJ+/+8hkg6NIg=; b=h4VDW10lGnAw 75KIUPE+knE2eGy9mlyGWbd0HaRPMo9cCVlE0s77FoQ5K98YlUgH4qGx8x4X5yPs rIY50WznYYpds8MdmhiJKcmC2crgvCnuLKwNvBAKmBr+BTg/U+vvkfr/cvuWsKNZ +Y37XxlFFvoOG5i2ElcdJ+LbDULFi+E= 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 E5A9C160146 for <62978@debbugs.gnu.org>; Fri, 21 Apr 2023 01:05:45 +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 01:05:43 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62978@debbugs.gnu.org> Subject: Date: Fri, 21 Apr 2023 01:05:22 +0200 Message-ID: <20230420230523.6648-5-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230420230523.6648-1-madalinionel.patrascu@mdc-berlin.de> References: <20230420230523.6648-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27578.003 X-TM-AS-Result: No-10--4.970700-5.000000 X-TMASE-MatchedRID: mGX4zkTg7WUPK2Dvdm/TZqoXHZz/dXlxuemKEMcWmztYC5LPd7Bvbb8F Hrw7frluf146W0iUu2uD0fiPNa0yFh1hN+DNBjvOa87CDXaKRVILwteD+QnyUBHfiujuTbedKZQ /22HSWdVO6Alj8NGlo5znJQM3RhC8w+noLBygYTjX3j/lf1V8LOTAXNPNyDOEzK0Oun7bPnyYDT IhMw3OOX0tCKdnhB58rqunC0VjNpOfop0ytGwvXiq2rl3dzGQ1GpeevGsoI5eVHdwdgzQnlFOOp kfOzc9aVybdUfq2Y+M8SW+pXzDDzZ6DKrCYJUhycwNc37gI45iNJiZ8TvheENh9cyxhiEM7cGJt inn115ANQSQFNny84vGXJMJdBHjGKgDk8Dh1C7G5iklHaSF5d37cGd19dSFd X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.970700-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27578.003 X-TM-SNTS-SMTP: AF7E10727D9522EF53C5D7425EBA520FCAF144D28B3489D61E9CE3757EE559BD2002:F X-Spam-Score: -0.3 (/) X-Debbugs-Envelope-To: 62978 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: -1.3 (-) Date: Fri, 21 Apr 2023 00:33:13 +0200 Subject: [PATCH 5/6] gnu: Add bpp-phyl-omics. * 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..93082d8814 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)) ;; I need to check this + (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. -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 20 19:06:06 2023 Received: (at 62978) by debbugs.gnu.org; 20 Apr 2023 23:06:06 +0000 Received: from localhost ([127.0.0.1]:38865 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppdLp-0007mh-PY for submit@debbugs.gnu.org; Thu, 20 Apr 2023 19:06:06 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:42087) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppdLg-0007l6-Tp for 62978@debbugs.gnu.org; Thu, 20 Apr 2023 19:05:57 -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=1682031946; x=1683846347; bh=xrJriJqiEFvX8kKs9XIzKbsIQmCc9rA5UKFlfDro16g=; b=A4wKAMoo6yhQ snyiEOektnSKQCLzDQix+dD1lsmj42YEfl5pfqvFktwGFnCSNiHnLHBl7LISlqPD KQ+RgGxU9sSvSrSlYuLQPFyvTQODBJ/peat9MlwKYkXVKndMFzzCYbUC0PgaMYCM a2XQ5/mblXfZDYP20U+i3tf979Ri/wY= 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 5C89216014E for <62978@debbugs.gnu.org>; Fri, 21 Apr 2023 01:05:46 +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 01:05:43 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62978@debbugs.gnu.org> Subject: Date: Fri, 21 Apr 2023 01:05:23 +0200 Message-ID: <20230420230523.6648-6-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230420230523.6648-1-madalinionel.patrascu@mdc-berlin.de> References: <20230420230523.6648-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27578.003 X-TM-AS-Result: No-10--3.100600-5.000000 X-TMASE-MatchedRID: htSXAp03950PK2Dvdm/TZqoXHZz/dXlxuemKEMcWmztYC5LPd7Bvbb8F Hrw7frluf146W0iUu2vNs+hSjQLHECq+GZ9ZHxIhuW77/y896sj4qCLIu0mtIPuzwJAEkzruTbI v25NGrv167OLuIAmsauhJuCRls/kQFLe/cH9ifKnX3j/lf1V8LAmWvXEqQTm5fL8fHUCAmutydo OwSW9CNZUNUXe7cYQD0Z64clgQMEWA1UdczcLx7lZ4U3MrW+XSsXVMcuyGnx0h+SjkHeEHtUp9E X9Zh2FufS0Ip2eEHnyuq6cLRWM2k5+inTK0bC9eKrauXd3MZDU5KxbzyvAKqHd7lpjcSJnYPZjj vujn1WCbXXgVUAl2e90Ac2DoGpq4uC7rkIOLpsG6mxARvIpmNJAQd9DvYrllyAWq3v5uMJEXU+j JKPJrMsel4d1cuMtvjvdbOxcC5/MQtmuxiADqhvKHck16UKN1GR8AXHcOfjI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.100600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27578.003 X-TM-SNTS-SMTP: 8BDB046D1EE53073B23602C0627AA9AB62B25D660F8068234E8791C97938CC382002:F X-Spam-Score: -0.3 (/) X-Debbugs-Envelope-To: 62978 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: -1.3 (-) Date: Fri, 21 Apr 2023 00:44:40 +0200 Subject: [PATCH 6/6] gnu: Add maffilter. * gnu/packages/bioinformatics.scm (maffilter): 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 93082d8814..c4cea24632 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6046,6 +6046,41 @@ (define-public macs sequencing tag position and orientation.") (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") -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 20 20:06:06 2023 Received: (at control) by debbugs.gnu.org; 21 Apr 2023 00:06:06 +0000 Received: from localhost ([127.0.0.1]:38911 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppeHu-000171-CH for submit@debbugs.gnu.org; Thu, 20 Apr 2023 20:06:06 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:54595) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppeHs-00016W-De for control@debbugs.gnu.org; Thu, 20 Apr 2023 20:06:04 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= mime-version:content-type:content-type:content-language :accept-language:message-id:date:date:subject:subject:from:from :received:received; s=mdc; t=1682035556; x=1683849957; bh=31Odxb v/NV8u++wp/KSF8jLtEWOMCwJrMvJd2B5YZq0=; b=nFUtXYU6vOP0deVuAGxwCL aB1Ur1TU7qHRmDSjELJnj5Ioy7JylUa5NSUfrW7+OG5WEAqCeW4r+nvdNi877VSs ehoAthTn7+k2C31ufD/lhxvX0TidD4huC1Rb3dJvxde3d1h/yespRQgxq4NlNo2B oTu/2Ca1Q+feUX9aeLHTo= 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 c2062.mx.srv.dfn.de (Postfix) with ESMTPS id D57F5300195 for ; Fri, 21 Apr 2023 02:05:56 +0200 (CEST) Received: from SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) 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 02:05:56 +0200 Received: from SW-IT-P-EX4.mdc-berlin.net ([fe80::e55f:895f:3b41:ec6a]) by SW-IT-P-EX4.mdc-berlin.net ([fe80::e55f:895f:3b41:ec6a%2]) with mapi id 15.01.2507.023; Fri, 21 Apr 2023 02:05:56 +0200 From: "MadalinIonel.Patrascu@mdc-berlin.de" To: "control@debbugs.gnu.org" Subject: control message for bug #62980 and #62978 Thread-Topic: control message for bug #62980 and #62978 Thread-Index: AQHZc+T5krzxNHW2nkSU6C8qGfZN6A== Date: Fri, 21 Apr 2023 00:05:56 +0000 Message-ID: <641438e8ad6e43ce85e505f242959209@mdc-berlin.de> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [141.80.113.51] x-tm-as-product-ver: SMEX-14.0.0.3092-9.0.1002-27578.003 x-tm-as-result: No-10--10.664600-5.000000 x-tmase-matchedrid: MnV6/QBRMnAaED+N1J68lsG0UNgaZpYqGsvgUMYAn4UWzPTbxO7R+tIS YzBUt2RaXVsEWVqYqaivJcrLMYkA70UuXkWTSi/R30kDaWZBE1RU4sxFq6igEUqa6TyhyXvPtAg K4TtXrP1GUsVNd0mL6QC2F/gPANDtCdtCev19Y1LZ6cd1XW8QucogYxpm9PTbAs7f5tvs5+iEIc UVoa0/oH0tCKdnhB58dcD5PxhxmQM+8FJNGdxYq80z+VHYZXoPZHgDHw9doex1gVIsurBVFv3y1 lL2MimFqKSa7+1FelwwPvERclccVw== x-tm-as-user-approved-sender: Yes x-tm-as-user-blocked-sender: No x-tmase-result: 10--10.664600-5.000000 x-tmase-version: SMEX-14.0.0.3092-9.0.1002-27578.003 x-tm-snts-smtp: 07AEA2113FA8D6F3927FA6FDB2DC3C509D7490B3AC348383D546BA6F18F129092002:F Content-Type: multipart/alternative; boundary="_000_641438e8ad6e43ce85e505f242959209mdcberlinde_" MIME-Version: 1.0 X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: control 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 (---) --_000_641438e8ad6e43ce85e505f242959209mdcberlinde_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable block 62980 by 62978 --_000_641438e8ad6e43ce85e505f242959209mdcberlinde_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

block 62980 by 62= 978

--_000_641438e8ad6e43ce85e505f242959209mdcberlinde_-- From debbugs-submit-bounces@debbugs.gnu.org Fri Apr 21 04:17:10 2023 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?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62978@debbugs.gnu.org> Subject: [PATCH v2 3/6] gnu: bpp-phyl: Update to 2.4.1. 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 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit 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-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 62978 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 (---) * 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 -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Fri Apr 21 04:17:11 2023 Received: (at 62978) by debbugs.gnu.org; 21 Apr 2023 08:17:11 +0000 Received: from localhost ([127.0.0.1]:39196 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pplx8-0000JX-QL for submit@debbugs.gnu.org; Fri, 21 Apr 2023 04:17:11 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:37909) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pplx4-0000IU-6e 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=1682065019; x=1683879420; bh=3NCbK+5cmWvKVDm62WmS9OQoUzC7qNcnUsKyRbBAlv4=; b=AQ8hF17Wl7iX QuJ9AzGM8sOY2k/d00CYac97GW1lJQkZAY8rSF9D0UcaQ7+pPVWNyzhpbL00Latp GYGP9Pl7TDYDub9DIwz3OtVpNpjyyIe29GV0ppOR4PYO35h6oQQe8sC8KMXk6ZxF 13vDN3Ge5sf9c43d9Sr90EE7fOZbrR8= 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 CC48716013D 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?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62978@debbugs.gnu.org> Subject: [PATCH v2 2/6] gnu: bpp-seq: Update to 2.4.1. Date: Fri, 21 Apr 2023 10:16:37 +0200 Message-ID: <20230421081641.18388-2-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 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit 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: jtEPcQmLSabBP9kF6SLh5hIRh9wkXSlFyiKgKtIyB4qAI7Mvq/sL54PN dYXFrfiyIVOe0TAdekipgf1jMun5ewV2NKF6aideEXjPIvKd74BMkOX0Uoduuc3wMjzgVvguChb 10lmaN/ZYzJcD0gVKSpzSLZJ1HkA9mv0Xhs8HK808o3fwIs8rQX607foZgOWypjlkbDvDJ4dU82 kILwgVLQ1RxwBNHJ3UnAr+uwKiSZatYv/FAmebjqubsOtSWY2QX7bicKxRIU1vsMcSUZ5eOa0hb OeGOMG1+gtHj7OwNO22utO5qEfOUS3tVRgNe77r6qroNo52d/NXBilH6tK8IMwrwh7pFUgn6gW0 gV3KLicnyZAOlHoct2jEk0CqmiY5YRakf5gBZpF3tp/9pMZkg3QJ88ZHP8DjvmJf6uotZp79Zjt YmCyQ6k+HGwSCjLh6vuvB6gAgryg= 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: CD07346E9D8DE40D276565DD36320FDD075265E81CE76DD4DA7ECD36485233A52002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 62978 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 (---) * gnu/packages/bioinformatics.scm (bpp-seq): 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. --- 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 -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Fri Apr 21 04:17:11 2023 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?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62978@debbugs.gnu.org> Subject: [PATCH v2 4/6] gnu: Add bpp-seq-omics. 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 Content-Transfer-Encoding: 8bit Content-Type: text/plain 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-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 62978 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 (---) * 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. -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Fri Apr 21 04:17:12 2023 Received: (at 62978) by debbugs.gnu.org; 21 Apr 2023 08:17:12 +0000 Received: from localhost ([127.0.0.1]:39200 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pplx9-0000Jn-NI for submit@debbugs.gnu.org; Fri, 21 Apr 2023 04:17:12 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:33523) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pplx5-0000Ir-Ad 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 :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1682065021; x=1683879422; bh=Yj6Fx2V6FdjJ0Tk UAOkRa0OtQOorE1n3R+cDP7NYNdY=; b=qNr71hdsf4vmd74LYW051+B6CaNolhW 5Th3YGoZ/Txltvwl+Yl9NZ/Fk7dGSw2YCpwailGBThpEQnuGL9KjGCUyhPvlJSF+ xOCZpLjFJX4Qr+aisQdCNrRsl07sbqf2jUsFd7TWXq8K3DCEHjZqXPfmT6n4TShd T9LPVYBtaRuQ= 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 8893C160146 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?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62978@debbugs.gnu.org> Subject: [PATCH v2 1/6] gnu: bpp-core: Update to 2.4.1. Date: Fri, 21 Apr 2023 10:16:36 +0200 Message-ID: <20230421081641.18388-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit 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--1.394100-5.000000 X-TMASE-MatchedRID: pZLUNb3bRHnBP9kF6SLh5hIRh9wkXSlFyiKgKtIyB4r4fBXFxNAfp97/ ybOnPpOWdv3Gh5XGj9rSnIV30zDy6i/7QU2czuUNA9lly13c/gEfNd74n18052mj1qXcLu1ii0x TsP0eePKgltKRXQwrjOZcMn+WYPb3SlvaILig77vX3j/lf1V8LPioIsi7Sa0g2bbiFWJldQ9a3X 1b/kjNbJtsS2JfHus3Gr4YPOFlg2WtYv/FAmebjjuUqTPTfDTr64sVlliWKx+/WXZS/HqJ2j++5 wafXR2mSnQ4MjwaO9cqtq5d3cxkNRqXnrxrKCOXFAIA8CD6mNWjSlFgiC4ai0FwPtkEyMOM3epP 3AqjoivYW+h4lZ5GBbpP5tFr3+rCyBPyIlr2B/10iEm2gU1CSs7diEIzl+rODUEkBTZ8vOLxlyT CXQR4xioA5PA4dQuxuYpJR2kheXd+3BndfXUhXQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.394100-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27578.006 X-TM-SNTS-SMTP: F40669D209DC724555D86F0F4BC908711FBF0952075D1DAA06B1502CD90534CB2002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 62978 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 (---) * gnu/packages/bioinformatics.scm (bpp-core): Update to 2.4.1. [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(-) 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 base-commit: 904b77e1814b611c256ecf161aa36f58d0882380 -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Fri Apr 21 04:17:20 2023 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?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62978@debbugs.gnu.org> Subject: [PATCH v2 5/6] gnu: Add bpp-phyl-omics. 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 Content-Transfer-Encoding: 8bit Content-Type: text/plain 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-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 62978 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 (---) * 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. -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Fri Apr 21 04:17:21 2023 Received: (at 62978) by debbugs.gnu.org; 21 Apr 2023 08:17:21 +0000 Received: from localhost ([127.0.0.1]:39206 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pplxI-0000KK-Lc for submit@debbugs.gnu.org; Fri, 21 Apr 2023 04:17:21 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:47601) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pplxB-0000JB-Eq for 62978@debbugs.gnu.org; Fri, 21 Apr 2023 04:17:14 -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=Tu23+bz62EJT9E3ZXytA4UEaYiMi/xsmSrFRXSkeSAY=; b=hQ5tffEEG6M7 6HMLGYXYCU5xuBkB9i+ymLT0RRCdOPjjEo+egXE9ENwMfVlsinS5tPX5Kbj6yZ4p MNCFwWxXwRf5dyPJinS6u9otsLVuwhIzFjnforKTXLCU53OGzIpQggeuDpAaqa25 giJISiXmNPA0Vk63rghFe8cAmRZTwvQ= 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 AD450160153 for <62978@debbugs.gnu.org>; Fri, 21 Apr 2023 10:17:02 +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 10:16:59 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62978@debbugs.gnu.org> Subject: [PATCH v2 6/6] gnu: Add maffilter. Date: Fri, 21 Apr 2023 10:16:41 +0200 Message-ID: <20230421081641.18388-6-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 Content-Transfer-Encoding: 8bit Content-Type: text/plain 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--2.216400-5.000000 X-TMASE-MatchedRID: kREspPIIG7R6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt10ieHN50/kHsZaZ5UBQsocxVUWGXs3C8+5SxpUwKMktuQs cbBntvLttyQQOVy5Jb41O+yFvbaN63PhwfmFb3ph0+657dxGJGI9I12PUkzIBTx7puPYIc8gU45 rKCfVRMbCzbsCrQmwFUTeAYq6/WpLGVX5bPZlV5ANykgdfrNyIPn/9u4K/no6XBXaJoB9JZxRFJ Jyf5BJe3QfwsVk0UbsiEonDMI2Cf7lX3Pe+qTcqyqYNYQrwrNV+FALouNvttzDWIbNbVazIryCO urifLH0CH0pNmn4aTM+Is80CvxHQVc4RnQIVfX19S3JqlRcHto6drh+sI/oAKEIODKywTy6jfJg lXzHQ6sxRVzSzXt2xf+rhMPa/srU= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.216400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27578.006 X-TM-SNTS-SMTP: CFDD4E03DD32E5CF78C93499BF8EC2E2BAEE8F786B90F916821E312F0CB3FB682002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 62978 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 (---) * gnu/packages/bioinformatics.scm (maffilter): 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 511431fb95..169ae39552 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6046,6 +6046,41 @@ (define-public macs sequencing tag position and orientation.") (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") -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Fri Apr 21 07:18:17 2023 Received: (at 62978-done) by debbugs.gnu.org; 21 Apr 2023 11:18:17 +0000 Received: from localhost ([127.0.0.1]:39463 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppomP-000622-9R for submit@debbugs.gnu.org; Fri, 21 Apr 2023 07:18:17 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21040) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ppomJ-00061q-QS for 62978-done@debbugs.gnu.org; Fri, 21 Apr 2023 07:18:16 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1682075888; cv=none; d=zohomail.com; s=zohoarc; b=JutFOcAQwEVZV5nJNIfrJQFkHwrCUTcXW6gvXauNH1Sw9JQFT3l54ULMoTM8AF0kv7w1qsY6WjpJo9NOjxrSQINGve+yW0jwyoCyTZKeypkZ9cX8f6LA1xS7H3NiQnM3OzxIz2AdDb6k9iTe0IX6cC5tkwe8Y3xhTQk4esu1F3w= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1682075888; h=Content-Type:Content-Transfer-Encoding:Date:From:MIME-Version:Message-ID:Subject:To; bh=GBwb/xqzKmJx/x7+YnvcPHmICj1TwOOe3Qy7pngZKHk=; b=FuJjqSHrBlaRVinJh0pYTLENmMVeRsGB4Nr5XAYIXY2KVg6YhA+xOIeYXyC2wWX77yZ7q3sGloz3P0Bikp2noycjcJCTBNfzhuEtb9l4pSUSIsG6MwTkk7oDyT1HsvfOBpap9nW+ga6SEoJu0TXyNBA5vpSUt0cp5e55PO5NOc8= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1682075888; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To:Cc; bh=GBwb/xqzKmJx/x7+YnvcPHmICj1TwOOe3Qy7pngZKHk=; b=JC9hkhpmAiy4t5bjM4Wy4uFTaNTv2vQOVJ8iz7Lt6jyBKl1UNMlNzFYzAVZH5T+I cnQqLJXhKBzYwHAgA8JX3Q7icO2rPJgeu6kZc4Pr6l6CWM3cyo8SvURIK5oiebUbJ7B d739H57g9zcvRGVS3DNpFrH78DxfepqK9ciH99d4= Received: from localhost (i5E862DF4.versanet.de [94.134.45.244]) by mx.zohomail.com with SMTPS id 1682075887317323.53206049429; Fri, 21 Apr 2023 04:18:07 -0700 (PDT) User-agent: mu4e 1.10.2; emacs 28.2 From: Ricardo Wurmus To: 62978-done@debbugs.gnu.org Subject: gnu: bpp-core, bpp-seq, bpp-phyl: Update to 2.4.1. && gnu: Add bpp-seq-omics, bpp-phyl-omics and maffilter. Date: Fri, 21 Apr 2023 13:16:37 +0200 Message-ID: <87cz3xpjpv.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 62978-done 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 (-) Thank you for these patches. I applied them. maffilter needed some changes: - formatting - license - git-fetch vs url-fetch (can=E2=80=99t use generated archive URLs) - sorting of inputs --=20 Ricardo From unknown Sat Sep 20 13:26:29 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Fri, 19 May 2023 11:24:10 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator