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Resent-From: Efraim Flashner Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 29 Jan 2023 13:13:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 61148 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 61148@debbugs.gnu.org Cc: Efraim Flashner Received: via spool by 61148-submit@debbugs.gnu.org id=B61148.167499797613719 (code B ref 61148); Sun, 29 Jan 2023 13:13:03 +0000 Received: (at 61148) by debbugs.gnu.org; 29 Jan 2023 13:12:56 +0000 Received: from localhost ([127.0.0.1]:42430 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pM7UN-0003Z4-JE for submit@debbugs.gnu.org; Sun, 29 Jan 2023 08:12:56 -0500 Received: from mail-ej1-f53.google.com ([209.85.218.53]:37433) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pM7UJ-0003YL-E7 for 61148@debbugs.gnu.org; Sun, 29 Jan 2023 08:12:51 -0500 Received: by mail-ej1-f53.google.com with SMTP id ud5so24963047ejc.4 for <61148@debbugs.gnu.org>; Sun, 29 Jan 2023 05:12:51 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:sender:from:to:cc:subject:date :message-id:reply-to; bh=YRttZ6A5URWe3rBjK6Cn62i95sXtm4invTeLsi0bA54=; b=AltrImexeI4CTT1qfE0q4Zaj5DjrpNOcy8ZU+9ovteOpa5hPmyxFgqGhpUOjQQ/mni oVnc+qadJ0vjUo0D8c0mJuwxyITOa+C5K5MkEpGAXrK5z2gw72KIjz7ouUKGFT93VZ0O 5q+b+Qkge2ELkRlvyja88J65os5D3iA/frhAjN+Rl1Pp30fk+ObCJQ//LeOSg6UvWwIz Gzm/gKCKtjHQmS6aZS3lP++k9I5Rx2HZ1NiWp3CJxAY9DQAcEoewM5nXp3gNbKqz22Wr cGNsa/VJjTvnaZHgLRJlv3fRAgPB+5u275bQ3i2I4OXGxTe4LYLUTk8cvVGHPtcOepdh bvCg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:sender:x-gm-message-state:from :to:cc:subject:date:message-id:reply-to; bh=YRttZ6A5URWe3rBjK6Cn62i95sXtm4invTeLsi0bA54=; b=VZOMEGDtghi5G5PEkQ19mQdN6nyqIlSXoQDRj/2FtU7TtmLsCdeC/sPb+q+7IFK17J 6hvsIfi3nAOldw1MZ8YT1VzJayf9ZHBfdu8QwE/2nrMu6F068IcGj3df3iJTvhGKIbmm KnrTOWXySniTbXpd/tfvcfKviVGkALcxbCUjpxgWWdfnwT8J4QtSj5Xs5qAF8N4h4kQO Eww3s02aV17WS2vxF2AcwmSzlFlCEF93prNk6++gAcUk2b2uc37QOl+HC1nd1cpHbj6/ Mw6UgzG5/3i+F30ENMaKA3tI8HY21+DFbYJKzoCPiO42DoNZkH/K+vFk9sJAcLHJVuQM dNmQ== X-Gm-Message-State: AO0yUKUI9eeovM0XOlL6JTWm5z2liPyjfQImoRZ2fQQRjlZsNVyLRZWg rRsUk0R4aGedRuY/DilYLnzSfJbVBSSCVQ== X-Google-Smtp-Source: AK7set9t6eQy1wp/yJxrkLY9cz1isT2TfI3U4/NETgRN/4KqcRO3BycO1YiPxSwqxSL+wxXLO5TlKw== X-Received: by 2002:a17:906:d8c4:b0:87f:546d:7cb5 with SMTP id re4-20020a170906d8c400b0087f546d7cb5mr7051789ejb.37.1674997965842; Sun, 29 Jan 2023 05:12:45 -0800 (PST) Received: from localhost ([141.226.15.115]) by smtp.gmail.com with ESMTPSA id p2-20020a1709060e8200b008786675d086sm5224765ejf.29.2023.01.29.05.12.45 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sun, 29 Jan 2023 05:12:45 -0800 (PST) From: Efraim Flashner Date: Sun, 29 Jan 2023 15:12:36 +0200 Message-Id: <8cd6e9d8b601af9fd507a60dd8efbd0b255eba96.1674997469.git.efraim@flashner.co.il> X-Mailer: git-send-email 2.39.1 In-Reply-To: References: MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (wfa2-lib): New variable. --- gnu/packages/bioinformatics.scm | 34 +++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fa0a6c0dd6..7b5d5c5e8c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15710,6 +15710,40 @@ (define-public tabixpp some of the details of opening and jumping in tabix-indexed files.") (license license:expat))) +(define-public wfa2-lib + (let ((commit "188b522ae634add3c692ca7547595b7266f1fa19") + (revision "1")) + (package + (name "wfa2-lib") + (version (git-version "2.3.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/smarco/WFA2-lib") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1pq844zsl7v5zk6pzkbh5j2k2g1ac54nlvgyihla2wlwi0ibndax")))) + (build-system cmake-build-system) + (arguments + (list + #:configure-flags + #~(list "-DOPENMP=ON"))) + (native-inputs + (list pkg-config)) + (home-page "https://github.com/ekg/tabixpp") + (synopsis "Wavefront alignment algorithm library") + (description "The @acronym{wavefront alignment, WFA} algorithm is an exact +gap-affine algorithm that takes advantage of homologous regions between the +sequences to accelerate the alignment process. Unlike to traditional dynamic +programming algorithms that run in quadratic time, the WFA runs in time +@code{O(ns+s^2)}, proportional to the sequence length @code{n} and the alignment +score @code{s}, using @code{O(s^2)} memory (or @code{O(s)} using the +ultralow/BiWFA mode). Moreover, the WFA algorithm exhibits simple computational +patterns that the modern compilers can automatically vectorize for different +architectures without adapting the code.") + (license license:expat)))) + (define-public smithwaterman (let ((commit "2610e259611ae4cde8f03c72499d28f03f6d38a7")) (package