From patchwork Thu Apr 20 23:05:23 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 49337 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 5999817585; Fri, 21 Apr 2023 00:07:45 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED autolearn=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 1BE691747E for ; Fri, 21 Apr 2023 00:07:43 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1ppdMo-0008BQ-FX; Thu, 20 Apr 2023 19:07:06 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ppdMn-0008AU-Qw for guix-patches@gnu.org; Thu, 20 Apr 2023 19:07:05 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ppdMl-0005HZ-2D for guix-patches@gnu.org; Thu, 20 Apr 2023 19:07:05 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1ppdMk-0007oP-Ti for guix-patches@gnu.org; Thu, 20 Apr 2023 19:07:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62978] Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 20 Apr 2023 23:07:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 62978 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <62978@debbugs.gnu.org> Received: via spool by 62978-submit@debbugs.gnu.org id=B62978.168203196629936 (code B ref 62978); Thu, 20 Apr 2023 23:07:02 +0000 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?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= 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 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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches 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")