From patchwork Fri Aug 5 09:33:03 2022 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: 41299 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 10F6227BBE9; Fri, 5 Aug 2022 10:36:05 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 5DF1827BBEB for ; Fri, 5 Aug 2022 10:36:04 +0100 (BST) Received: from localhost ([::1]:55062 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1oJtkR-0003gq-DY for patchwork@mira.cbaines.net; Fri, 05 Aug 2022 05:36:03 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:48800) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oJtiV-0003f3-4G for guix-patches@gnu.org; Fri, 05 Aug 2022 05:34:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:38254) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1oJtiU-0000Zn-Cx for guix-patches@gnu.org; Fri, 05 Aug 2022 05:34:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1oJtiU-0007lA-2K; Fri, 05 Aug 2022 05:34:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#56999] [PATCH 1/4] gnu: Add phyml. References: <398fc66441a34468a7c66370abb8f923@mdc-berlin.de> In-Reply-To: <398fc66441a34468a7c66370abb8f923@mdc-berlin.de> Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Fri, 05 Aug 2022 09:34:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 56999 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <56999@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 56999-submit@debbugs.gnu.org id=B56999.165969200629756 (code B ref 56999); Fri, 05 Aug 2022 09:34:02 +0000 Received: (at 56999) by debbugs.gnu.org; 5 Aug 2022 09:33:26 +0000 Received: from localhost ([127.0.0.1]:56229 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oJthu-0007jn-2k for submit@debbugs.gnu.org; Fri, 05 Aug 2022 05:33:26 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:55105) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oJths-0007jR-BH for 56999@debbugs.gnu.org; Fri, 05 Aug 2022 05:33:24 -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 :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1659691998; x=1661506399; bh=MYPDRqRBMPBzjhy J5rlGJgea7o/YW10nPogDJbR5Xx0=; b=PgSptdEBMst4W34omHdXem+o/2e091l l2ywwA33VQXAf7QoSbv97Vop8i8uvi9PWFi6AU4mHmRBVKhb9OHVVpPNuwd1MKUH zWkXhU1D928m4/1kwenUWDjl0mFSMR8ATcBhGYD3qVSXT3GcCCgJWRKLitafj5YH Xw56VmeCbxkc= 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 49F52160390 for <56999@debbugs.gnu.org>; Fri, 5 Aug 2022 11:33:18 +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 15.1.2507.9; Fri, 5 Aug 2022 11:33:17 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Fri, 5 Aug 2022 11:33:03 +0200 Message-ID: <20220805093306.21767-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.1 MIME-Version: 1.0 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-14.0.0.3092-9.0.1002-27058.006 X-TM-AS-Result: No-10--6.417000-5.000000 X-TMASE-MatchedRID: huMMtcahIlB6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VIpb wG9fIuITWtKJ53YwGGLuNT8xdcEnQwE+dA3RWUSvnVTWWiNp+v/KIqAq0jIHisIubEPSkNnJli+ BaqMwTNo+LWiWMkbaVlai9f4ppdhS74MThWsvfJhi71i5on34Kj7xZyBSNBTCfw+FWPV9n7q+oA mvH3qvXYOaK7R6v2MMDKhMD70B3lMxzpurb8CqYHsZMBX90xmm1+Cp0Qg3BZ4OUs4CTUgKy1N+F 8fdIPkCYn6cI9w5Vog9hU++cg3wZdaVXJCx4JNCq5uw61JZjZCAMuqetGVetnyef22ep6XYymsk /wUE4hrE/GgTDPZQO62t1xaPjrRuM+zy/fYYl0W43+2so7gAwd4BhmE4Jsgh X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.417000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27058.006 X-TM-SNTS-SMTP: 3D47BE18CC7E45723E37BB8372FAF3D1F9EE361D4C7D82E3B046D21648BE24E12002: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" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (phyml): New variable. --- gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) base-commit: 47a38d09696b309f6174b585465e621352444ddb diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 00238531db..fa91f48569 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9068,6 +9068,43 @@ (define-public phylip programs for inferring phylogenies (evolutionary trees).") (license license:bsd-2))) +(define-public phyml + (package + (name "phyml") + (version "3.3.20220408") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/stephaneguindon/phyml") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "03hdqmnsgnzkcrp9r9ajdfkj33jgq4b86kra8ssjlrph65y344sa")))) + (build-system gnu-build-system) + (native-inputs + (list automake + autoconf)) + (home-page "https://github.com/stephaneguindon/phyml") + (synopsis "Programs for working on SAM/BAM files") + (description + "@code{PhyML} is a software package that uses modern statistical approaches +to analyse alignments of nucleotide or amino acid sequences in a phylogenetic +framework. The main tool in this package builds phylogenies under the maximum +likelihood criterion. It implements a large number of substitution models coupled +with efficient options to search the space of phylogenetic tree topologies. @code{ +PhyTime} is another tool in the @code{PhyML} package that focuses on divergence +date estimation in a Bayesian setting. The main strengths of @code{PhyTime} lie +in its ability to accommodate for uncertrainty in the placement of fossil +calibration and the use of realistic models of rate variation along the tree. +Finally, code{PhyREX} fits the spatial-Lambda-Fleming-Viot model to geo-referenced +genetic data. This model is similar to the structured coalescent but assumes that +individuals are distributed along a spatial continuum rather than discrete demes. +@code{PhyREX} can be used to estimate population densities and rates of dispersal. +Its output can be processed by treeannotator (from the @code{BEAST} package) as +well as @code{SPREAD}.") + (license license:gpl3))) + (define-public imp (package (name "imp") From patchwork Fri Aug 5 09:33:04 2022 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: 41297 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 77BD927BBEC; Fri, 5 Aug 2022 10:36:04 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 32F5027BBE9 for ; Fri, 5 Aug 2022 10:36:04 +0100 (BST) Received: from localhost ([::1]:55064 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1oJtkR-0003gr-61 for patchwork@mira.cbaines.net; Fri, 05 Aug 2022 05:36:03 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:48802) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oJtiV-0003f4-4T for guix-patches@gnu.org; Fri, 05 Aug 2022 05:34:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:38257) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1oJtiU-0000Zo-Hp for guix-patches@gnu.org; Fri, 05 Aug 2022 05:34:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1oJtiU-0007lJ-E3; Fri, 05 Aug 2022 05:34:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#56999] [PATCH 2/4] gnu: Add phyml-mpi. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Fri, 05 Aug 2022 09:34:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 56999 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <56999@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 56999-submit@debbugs.gnu.org id=B56999.165969200929772 (code B ref 56999); Fri, 05 Aug 2022 09:34:02 +0000 Received: (at 56999) by debbugs.gnu.org; 5 Aug 2022 09:33:29 +0000 Received: from localhost ([127.0.0.1]:56232 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oJthw-0007k6-K4 for submit@debbugs.gnu.org; Fri, 05 Aug 2022 05:33:28 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:41859) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oJtht-0007jS-0c for 56999@debbugs.gnu.org; Fri, 05 Aug 2022 05:33:25 -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=1659691999; x=1661506400; bh=jdFkWR08uzTCKUQpeTPwbe9guWdn6Say5qgpCfx8/bk=; b=Dhdaoh/+AIjA qsXovmEMQ4h7B0f18XAJvJP5fdng+pje4ps6SHnEBGi5icLFRP5PXGNlzxSETNHT bZBBDo/6VXXFcdl4NMLUYPMKarCcN0z2UjIuOaUuAbOMa9w/oExzcNshtcGz4y/4 2Yy/dRk3VpH1JNp469ykYZIvEvaYN3g= 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 03B56160394 for <56999@debbugs.gnu.org>; Fri, 5 Aug 2022 11:33:19 +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 15.1.2507.9; Fri, 5 Aug 2022 11:33:18 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Fri, 5 Aug 2022 11:33:04 +0200 Message-ID: <20220805093306.21767-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.1 In-Reply-To: <20220805093306.21767-1-madalinionel.patrascu@mdc-berlin.de> References: <20220805093306.21767-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 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-14.0.0.3092-9.0.1002-27058.006 X-TM-AS-Result: No-10-0.190300-5.000000 X-TMASE-MatchedRID: BrKfIHwbYjV6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VDI3 NdfFmGpMfS0Ip2eEHnwj/1Rbkzl1E95/HgWYxplM5MIx11wv+CPKayT/BQTiGk8XOMKR+RhSrDX lnqrP39YoWwp6YEIz4HLwQmh72397ISTtzMCCKYWgiZqDH7QQVDg8YCmQy4oAqVjwx1umPUCoo7 lRIplgTMWDv2TYRvIltOdWe/Uk/vuwZO9kmaWWvP8+E8vSQCkfySOb56URxsg= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.190300-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27058.006 X-TM-SNTS-SMTP: A535829A769EC6E2C7DBD4DB107D8D3B764048CB37FEC02EA526826DCF988DB72002: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" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (phyml-mpi): New variable. --- gnu/packages/bioinformatics.scm | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fa91f48569..f448341031 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9105,6 +9105,17 @@ (define-public phyml well as @code{SPREAD}.") (license license:gpl3))) +(define-public phyml-mpi + (package (inherit phyml) + (name "phyml-mpi") + (arguments + `(#:configure-flags + (list "--enable-phyml-mpi"))) + (native-inputs + (list autoconf + automake + openmpi)))) + (define-public imp (package (name "imp") From patchwork Fri Aug 5 09:33:05 2022 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: 41298 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 CB64327BBE9; Fri, 5 Aug 2022 10:36:04 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 55F5127BBEA for ; Fri, 5 Aug 2022 10:36:04 +0100 (BST) Received: from localhost ([::1]:55060 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1oJtkR-0003gk-D8 for patchwork@mira.cbaines.net; Fri, 05 Aug 2022 05:36:03 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:48804) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oJtiV-0003f5-7V for guix-patches@gnu.org; Fri, 05 Aug 2022 05:34:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:38258) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1oJtiU-0000Zq-Uv for guix-patches@gnu.org; Fri, 05 Aug 2022 05:34:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1oJtiU-0007lR-PJ; Fri, 05 Aug 2022 05:34:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#56999] [PATCH 3/4] gnu: Add phyml-phyrex. 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charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 41300 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 D72CB27BBEA; Fri, 5 Aug 2022 10:39:16 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 3235F27BBE9 for ; Fri, 5 Aug 2022 10:39:13 +0100 (BST) Received: from localhost ([::1]:58112 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1oJtnU-00066L-BD for patchwork@mira.cbaines.net; Fri, 05 Aug 2022 05:39:12 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:48806) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oJtiV-0003f6-GM for guix-patches@gnu.org; Fri, 05 Aug 2022 05:34:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:38261) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1oJtiV-0000a2-8W for guix-patches@gnu.org; Fri, 05 Aug 2022 05:34:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1oJtiV-0007lZ-4d; Fri, 05 Aug 2022 05:34:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#56999] [PATCH 4/4] nu: Add phyml-rf. 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