From nobody Mon Jan 30 19:09:52 2023 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 4P5Hmx0sc3z3cGX5; Mon, 30 Jan 2023 19:09:53 +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 4P5Hmx0NLJz3j3j; Mon, 30 Jan 2023 19:09:53 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1675105793; 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=DmCAXtu1PHbGbGpzxa+tb8EOkZOwcZOTkdJPedB3vzk=; b=CCmIgcMuzBWzZsdD4Ziyq3gJ+slcvkZ2OPGXj6laI0peyV9QgvM5ktve0/UoYTOLU8P7/q EbXLL3nrcp2JH4XTl4zUKx7ktMDOMptfwDEeSG7RNE20RK6fpw8HBUY5+/kCQ+bFhxYJfI UzKR2TJWNUnD2RfGwnEwOamk8rkXq//tFV3edWmUEVVUF7HBmY9O5OnjXFIgSyRxf/+yUc wFJAwd3/wu4ny/c3RK9tJxK+tog/JuVGpe4drG/HMMZS0miiQ/lu1KOE8uBZqfL5FHU2YA OZgjgnqG5GvT5IzPSn3of1X3yqEZ7fR65TvuMlIAS4y4zLI8d9KLhsFMiHQGiw== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1675105793; 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=DmCAXtu1PHbGbGpzxa+tb8EOkZOwcZOTkdJPedB3vzk=; b=EvH6I/gxaJFmn1RqTOlAceawgwgPvnNZBefK+5yF6hsX2AxoQgpvHZtf0/seuWrLYL+HOA u4/FFyfPrOo0YClTsFxws53Qfb7buOrVkr1Z45RHS2p9ifuVmrZz6VSDq35vuAsuEPcFSP RQfY7PbBFHZzCTan9K6ZzE9NYg+NF47FZRwTAMlqD93HQ3RmIcUU5qVTykFs2WJsV/gP2Z gW4/s50BX6hH3Id0s/qrFkXVo6363P7xhWqz88Hzrn9veletHiZhwlrd52+GRFYWb8aIem GWWupboMTaqPLpMqmcoG5rBJUZwShNWBQaAbeYgTTDd2n113ZKSPUWVuhrt2pw== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1675105793; a=rsa-sha256; cv=none; b=mYSBIoId0u4/z6YkxlLEwUvie1jDG1tn+ITvYzjG/On6WXFruZnMFqnahYeY4cP5wxOX58 IUPIKmyguFbUP+cz+6c3FrlmJiNj49pmbIh/N+An5gR8jZzHdab0AXkkD3iNfxGDMtf63A EYuVAqCBE9q+e1RgCkhbUYtmtjvRVS7cOIC87im3a2y9daF/KPDCZl918mQjMUCIt7mc5B Vw60F9fEJEN12FMDtOOnE8FjfrmBoCy//r/QCzR72+rg4TkOnrHMJO78+W4gqZs6KeaRZZ QY9bdUOn0qsM6uFH5N1cuwDqrEqO0yfHakSh+IH9KURlw/wcT29JGALf+dwPtQ== 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 4P5Hmw6Y2szK1B; Mon, 30 Jan 2023 19:09:52 +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 30UJ9q7B089821; Mon, 30 Jan 2023 19:09:52 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 30UJ9qsU089820; Mon, 30 Jan 2023 19:09:52 GMT (envelope-from git) Date: Mon, 30 Jan 2023 19:09:52 GMT Message-Id: <202301301909.30UJ9qsU089820@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: 595d0dabcfdc - main - biology/wfa2-lib: Exact gap-affine algorithm using homology 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: 595d0dabcfdc4e4a2eefbfff154f7c2ab04488be Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=595d0dabcfdc4e4a2eefbfff154f7c2ab04488be commit 595d0dabcfdc4e4a2eefbfff154f7c2ab04488be Author: Jason W. Bacon AuthorDate: 2023-01-30 19:09:02 +0000 Commit: Jason W. Bacon CommitDate: 2023-01-30 19:09:02 +0000 biology/wfa2-lib: Exact gap-affine algorithm using homology The 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 traditional dynamic programming algorithms that run in quadratic time, the WFA runs in time O(ns+s^2), proportional to the sequence length n and the alignment score s, using O(s^2) memory (or 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. --- biology/Makefile | 1 + biology/wfa2-lib/Makefile | 20 ++++++++++ biology/wfa2-lib/distinfo | 3 ++ .../wfa2-lib/files/patch-system_profiler__timer.h | 10 +++++ biology/wfa2-lib/pkg-descr | 9 +++++ biology/wfa2-lib/pkg-plist | 46 ++++++++++++++++++++++ 6 files changed, 89 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 801bff937770..43439e1f4a89 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -238,6 +238,7 @@ SUBDIR += viennarna SUBDIR += vsearch SUBDIR += vt + SUBDIR += wfa2-lib SUBDIR += wise .include diff --git a/biology/wfa2-lib/Makefile b/biology/wfa2-lib/Makefile new file mode 100644 index 000000000000..cb334b9bf0c3 --- /dev/null +++ b/biology/wfa2-lib/Makefile @@ -0,0 +1,20 @@ +PORTNAME= wfa2-lib +DISTVERSIONPREFIX= v +DISTVERSION= 2.3.2 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Exact gap-affine algorithm using homology to accelerate alignment +WWW= https://github.com/smarco/WFA2-lib + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE + +USES= cmake pkgconfig +USE_GITHUB= yes +USE_LDCONFIG= yes + +GH_ACCOUNT= smarco +GH_PROJECT= WFA2-lib + +.include diff --git a/biology/wfa2-lib/distinfo b/biology/wfa2-lib/distinfo new file mode 100644 index 000000000000..09a5d3555324 --- /dev/null +++ b/biology/wfa2-lib/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1675088499 +SHA256 (smarco-WFA2-lib-v2.3.2_GH0.tar.gz) = 310e3886506ab57d04205cdf5fed3ef31969ce39e9c6d341fd5c8a0d4aa0830b +SIZE (smarco-WFA2-lib-v2.3.2_GH0.tar.gz) = 4150874 diff --git a/biology/wfa2-lib/files/patch-system_profiler__timer.h b/biology/wfa2-lib/files/patch-system_profiler__timer.h new file mode 100644 index 000000000000..5ebce4ad2b2e --- /dev/null +++ b/biology/wfa2-lib/files/patch-system_profiler__timer.h @@ -0,0 +1,10 @@ +--- system/profiler_timer.h.orig 2023-01-30 14:47:11 UTC ++++ system/profiler_timer.h +@@ -33,6 +33,7 @@ + #ifndef PROFILER_TIMER_H + #define PROFILER_TIMER_H + ++#include // Required on FreeBSD 12.3 + #include "profiler_counter.h" + + /* diff --git a/biology/wfa2-lib/pkg-descr b/biology/wfa2-lib/pkg-descr new file mode 100644 index 000000000000..24a0b82a109e --- /dev/null +++ b/biology/wfa2-lib/pkg-descr @@ -0,0 +1,9 @@ +The 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 traditional +dynamic programming algorithms that run in quadratic time, the WFA runs +in time O(ns+s^2), proportional to the sequence length n and the +alignment score s, using O(s^2) memory (or 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. diff --git a/biology/wfa2-lib/pkg-plist b/biology/wfa2-lib/pkg-plist new file mode 100644 index 000000000000..235ff54015ca --- /dev/null +++ b/biology/wfa2-lib/pkg-plist @@ -0,0 +1,46 @@ +include/wfa2lib/alignment/affine2p_penalties.h +include/wfa2lib/alignment/affine_penalties.h +include/wfa2lib/alignment/cigar.h +include/wfa2lib/alignment/linear_penalties.h +include/wfa2lib/alignment/score_matrix.h +include/wfa2lib/system/mm_allocator.h +include/wfa2lib/system/mm_stack.h +include/wfa2lib/system/profiler_counter.h +include/wfa2lib/system/profiler_timer.h +include/wfa2lib/utils/bitmap.h +include/wfa2lib/utils/commons.h +include/wfa2lib/utils/dna_text.h +include/wfa2lib/utils/heatmap.h +include/wfa2lib/utils/sequence_buffer.h +include/wfa2lib/utils/string_padded.h +include/wfa2lib/utils/vector.h +include/wfa2lib/wavefront/wavefront.h +include/wfa2lib/wavefront/wavefront_align.h +include/wfa2lib/wavefront/wavefront_aligner.h +include/wfa2lib/wavefront/wavefront_attributes.h +include/wfa2lib/wavefront/wavefront_backtrace.h +include/wfa2lib/wavefront/wavefront_backtrace_buffer.h +include/wfa2lib/wavefront/wavefront_backtrace_offload.h +include/wfa2lib/wavefront/wavefront_bialign.h +include/wfa2lib/wavefront/wavefront_bialigner.h +include/wfa2lib/wavefront/wavefront_components.h +include/wfa2lib/wavefront/wavefront_compute.h +include/wfa2lib/wavefront/wavefront_compute_affine.h +include/wfa2lib/wavefront/wavefront_compute_affine2p.h +include/wfa2lib/wavefront/wavefront_compute_edit.h +include/wfa2lib/wavefront/wavefront_compute_linear.h +include/wfa2lib/wavefront/wavefront_debug.h +include/wfa2lib/wavefront/wavefront_display.h +include/wfa2lib/wavefront/wavefront_extend.h +include/wfa2lib/wavefront/wavefront_heuristic.h +include/wfa2lib/wavefront/wavefront_offset.h +include/wfa2lib/wavefront/wavefront_pcigar.h +include/wfa2lib/wavefront/wavefront_penalties.h +include/wfa2lib/wavefront/wavefront_plot.h +include/wfa2lib/wavefront/wavefront_slab.h +include/wfa2lib/wavefront/wavefront_unialign.h +include/wfa2lib/wavefront/wfa.h +include/wfa2lib/wavefront/wfa.hpp +lib/libwfa2.a +lib/libwfa2.so +lib/libwfa2.so.0