From patchwork Thu Mar 31 07:28:49 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 38243 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 2A07927BBE9; Thu, 31 Mar 2022 08:31:08 +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 BFE6827BBEA for ; Thu, 31 Mar 2022 08:31:07 +0100 (BST) Received: from localhost ([::1]:55002 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nZpGs-0007Fg-Ja for patchwork@mira.cbaines.net; Thu, 31 Mar 2022 03:31:06 -0400 Received: from eggs.gnu.org ([209.51.188.92]:46786) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nZpFs-0006kF-0S for guix-patches@gnu.org; Thu, 31 Mar 2022 03:30:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43749) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nZpFr-000694-Mr for guix-patches@gnu.org; Thu, 31 Mar 2022 03:30:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nZpFr-0004TM-AN for guix-patches@gnu.org; Thu, 31 Mar 2022 03:30:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#54635] [PATCH v2 5/5] gnu: Add wfmash. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 31 Mar 2022 07:30:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 54635 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Efraim Flashner , Maxime Devos Cc: 54635@debbugs.gnu.org, Arun Isaac Received: via spool by 54635-submit@debbugs.gnu.org id=B54635.164871175317079 (code B ref 54635); Thu, 31 Mar 2022 07:30:03 +0000 Received: (at 54635) by debbugs.gnu.org; 31 Mar 2022 07:29:13 +0000 Received: from localhost ([127.0.0.1]:37640 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nZpF2-0004RK-S8 for submit@debbugs.gnu.org; Thu, 31 Mar 2022 03:29:13 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:51822) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nZpEx-0004Qf-2W for 54635@debbugs.gnu.org; Thu, 31 Mar 2022 03:29:08 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Transfer-Encoding:MIME-Version: References:In-Reply-To:Message-Id:Date:Subject:Cc:To:From:Sender:Reply-To: Content-Type:Content-ID:Content-Description:Resent-Date:Resent-From: Resent-Sender:Resent-To:Resent-Cc:Resent-Message-ID:List-Id:List-Help: List-Unsubscribe:List-Subscribe:List-Post:List-Owner:List-Archive; bh=qdxbq1pvz3OvQqxf4iO+hoUkerdg5PrwZlSuFuVyO6I=; b=W6imaFCsxxe6fqOSS8UoOY0lIj 5paIlTeGF0GLeKVoB13rj91PBYH+VxpZTtC6QlI4XdLPfy7CgxecxolLZoiu2hyGQpkR66nhvERET 9H9tbAZAlvJXifTnW65TSmKITcw8LvjOaCWZScJYUjTfXsEuaJEeMoTTnH+0ITyZPtHKGauAltPtz gDKRUgJVQ79xITQhLt3HpN/LTmjeLE3+QBinMNTiNizSbzSmJCqytMXLUaDEPNmaYE2vKzeNPogDT jzij9+j2Y1t8jhhthQsblwzIWadsNju+YPpT+5XP4kcHD+YTNm3mfiyUMJLLa9MLQrXpL4g4J3DyI wTyptS3g==; Received: from [192.168.2.1] (port=47376 helo=localhost.localdomain) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.95) (envelope-from ) id 1nZpEi-000V88-Lq; Thu, 31 Mar 2022 12:58:52 +0530 From: Arun Isaac Date: Thu, 31 Mar 2022 12:58:49 +0530 Message-Id: <20220331072849.22417-5-arunisaac@systemreboot.net> X-Mailer: git-send-email 2.34.0 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" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (wfmash): New variable. --- gnu/packages/bioinformatics.scm | 51 +++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2f6f3efb66..500ba4ac60 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16107,3 +16107,54 @@ (define-public ccwl @acronym{EDSL, Embedded Domain Specific Language} in the Scheme programming language.") (license license:gpl3+))) + +(define-public wfmash + (package + (name "wfmash") + (version "0.8.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/ekg/wfmash/releases/download/v" + version "/wfmash-v" version ".tar.gz")) + (sha256 + (base32 + "031cm1arpfckvihb28vlk69mirpnmlag81zcscfba1bac58wvr7c")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Unbundle atomic-queue. + (delete-file-recursively "src/common/atomic_queue") + (substitute* "src/align/include/computeAlignments.hpp" + (("\"common/atomic_queue/atomic_queue.h\"") + "")))))) + (build-system cmake-build-system) + (arguments + `(#:tests? #f ; no tests + #:phases + (modify-phases %standard-phases + ;; Remove compiler flags and checks specific to x86 when not + ;; targeting it. + ,@(if (target-x86-64?) + '() + '((add-after 'unpack 'remove-x86-specific-compile-flags + (lambda _ + (substitute* (find-files "." "CMakeLists\\.txt") + (("-mcx16") "") + (("-march=native") "")) + (substitute* "src/common/dset64.hpp" + (("!__x86_64__") "0"))))))))) + (inputs + (list atomic-queue + gsl + htslib + jemalloc + zlib)) + (synopsis "Base-accurate DNA sequence aligner") + (description "@code{wfmash} is a DNA sequence read mapper based on mash +distances and the wavefront alignment algorithm. It is a fork of MashMap that +implements base-level alignment via the wflign tiled wavefront global +alignment algorithm. It completes MashMap with a high-performance alignment +module capable of computing base-level alignments for very large sequences.") + (home-page "https://github.com/ekg/wfmash") + (license license:expat)))