From nobody Tue Nov 22 16:39:24 2022 X-Original-To: dev-commits-ports-main@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4NGqj83ys7z4j2ZX; Tue, 22 Nov 2022 16:39:24 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4NGqj83N4tz3NYn; Tue, 22 Nov 2022 16:39:24 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1669135164; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=7yLMZGRsGc8S739HOZxONeIY3HlQKarXcVWvijbcBQE=; b=JID5hMx5P/EuDBC+q/k5sjP5SeRaYtByt9YxQbE2splxwCkZPp9kkJTCtr9NsbHTIWaW7l HUwSuHwsF3XO7A2hvfvj8G5hDa+I2XZC18IcPC3uaRoxk9lsdAgEE7YTN3sp7soLjpt67c Z1GAqWTuDJB8aLHpdIqn1eeQ8DoLFZhpOPFHFlpO8Y+EUbto+A/4GDjXMizvGSym6c6YDD G11z4G/cGvXIXGCo3ZpQb6kHJvGKFl6lyQQVsEWbdV0nXMW0vhfr7duJ0VQmd7wDGDHebl hFFlI5X/lpZausCRiwYI3VY5iBA0wtIutR3Njhjj7aTBjVCqW+NHfzXlGxPmFQ== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1669135164; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=7yLMZGRsGc8S739HOZxONeIY3HlQKarXcVWvijbcBQE=; b=ghH5L5LJW5KQJJhSMRWA9zgCSyy3a7vraAaJMUdU3CdKqD5nU2Cms4vJs6EjLtsX4qBRhr LeSBJF8+uh1gvSNFoogGFXL0l7ik5dPS+bLKVUjd2B/zj0mb6UhioFbZVWN8KJstay8MdS 3gOMY8PITfmELp5WZ+DOx16TeDmCUq2y1FRV80vZ7g8dQ/eUtJ5KsKV/L0HcIN7PPKHfl0 2H6T23o06HngJSytM4abVEWN6aObikmZpUOSmsBb0e4LSkIKJQms1UuXT/s4UZEyHwOlp7 I1zdiMI/T1zI/jUCSK+0qmcpRnCl7lycSWKeZZJzwLw4Ktl1x2mAzdFHpdBrgg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1669135164; a=rsa-sha256; cv=none; b=vzbbvs73jOQK4mWFaN7ZGo5l5KuMnekkpMs6isDPdcaGo01M/B8F6un1xvYeWuwbKAfFL4 IEhOmD6cRiF3d8Y4Se0ZVRKfOPG03hlPBxNaSEbMQN+9oA4YkbRPHUQ+MI8o5KKoxSRZJw J1QpjhLn3UkMrcFsUrN8c4nbD3Q21f9Wn2ajTh4kFbm83KvoS1Hhrr7A0gUkaQGWhHAFtW cO5Qvs+cyX4qw6sLCuqLPvNSt2UifoLzIMGiHzTM5zere5lYAacLFEZV5z9f0N1M0u3dDl u255ifD+3PueFX3zjB9sxeo1ntwVyyL25x8c7OfHFvyIVO2qJzZHoRU0qYkhqA== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4NGqj82PzXzpdX; Tue, 22 Nov 2022 16:39:24 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 2AMGdO4x054995; Tue, 22 Nov 2022 16:39:24 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 2AMGdOi4054994; Tue, 22 Nov 2022 16:39:24 GMT (envelope-from git) Date: Tue, 22 Nov 2022 16:39:24 GMT Message-Id: <202211221639.2AMGdOi4054994@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: acb3a0de6468 - main - biology/megahit: Ultra-fast single-node metagenomics assembly List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: acb3a0de6468b1fe930e53af1894505e9b8d64c7 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=acb3a0de6468b1fe930e53af1894505e9b8d64c7 commit acb3a0de6468b1fe930e53af1894505e9b8d64c7 Author: Jason W. Bacon AuthorDate: 2022-11-22 16:38:31 +0000 Commit: Jason W. Bacon CommitDate: 2022-11-22 16:39:22 +0000 biology/megahit: Ultra-fast single-node metagenomics assembly MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG contstruction. --- biology/Makefile | 1 + biology/megahit/Makefile | 23 +++++++++++++++++++++++ biology/megahit/distinfo | 3 +++ biology/megahit/pkg-descr | 4 ++++ biology/megahit/pkg-plist | 14 ++++++++++++++ 5 files changed, 45 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 25ed50f54925..2ba55e0738ae 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -90,6 +90,7 @@ SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 + SUBDIR += megahit SUBDIR += migrate SUBDIR += minimap2 SUBDIR += mmseqs2 diff --git a/biology/megahit/Makefile b/biology/megahit/Makefile new file mode 100644 index 000000000000..30080e9d2564 --- /dev/null +++ b/biology/megahit/Makefile @@ -0,0 +1,23 @@ +PORTNAME= megahit +DISTVERSIONPREFIX= v +DISTVERSION= 1.2.9 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Ultra-fast single-node large and complex metagenomics assembly +WWW= https://github.com/voutcn/megahit + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE + +ONLY_FOR_ARCHS= amd64 powerpc64 powerpc64le riscv64 +ONLY_FOR_ARCHS_REASON= "Uses specific 64-bit CPU features" + +USES= cmake python shebangfix +SHEBANG_FILES= src/megahit +USE_GITHUB= yes +GH_ACCOUNT= voutcn + +CFLAGS+= -pthread + +.include diff --git a/biology/megahit/distinfo b/biology/megahit/distinfo new file mode 100644 index 000000000000..a70a74294d7a --- /dev/null +++ b/biology/megahit/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1669058254 +SHA256 (voutcn-megahit-v1.2.9_GH0.tar.gz) = 09026eb07cc4e2d24f58b0a13f7a826ae8bb73da735a47cb1cbe6e4693118852 +SIZE (voutcn-megahit-v1.2.9_GH0.tar.gz) = 268591 diff --git a/biology/megahit/pkg-descr b/biology/megahit/pkg-descr new file mode 100644 index 000000000000..8bf2914062fd --- /dev/null +++ b/biology/megahit/pkg-descr @@ -0,0 +1,4 @@ +MEGAHIT is a single node assembler for large and complex metagenomics NGS +reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve +low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to +accelerate its SdBG contstruction. diff --git a/biology/megahit/pkg-plist b/biology/megahit/pkg-plist new file mode 100644 index 000000000000..cda27e5d670d --- /dev/null +++ b/biology/megahit/pkg-plist @@ -0,0 +1,14 @@ +bin/megahit +bin/megahit_core +bin/megahit_core_no_hw_accel +bin/megahit_core_popcnt +bin/megahit_toolkit +%%DATADIR%%/test_data/empty.fa +%%DATADIR%%/test_data/generate_random_fasta.py +%%DATADIR%%/test_data/loop.fa +%%DATADIR%%/test_data/r1.il.fa.gz +%%DATADIR%%/test_data/r2.il.fa.bz2 +%%DATADIR%%/test_data/r3_1.fa +%%DATADIR%%/test_data/r3_2.fa +%%DATADIR%%/test_data/r4.fa +%%DATADIR%%/test_data/ref.fa