From owner-dev-commits-ports-all@freebsd.org Thu Jun 24 17:32:14 2021 Return-Path: Delivered-To: dev-commits-ports-all@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id E9AD76514BD; Thu, 24 Jun 2021 17:32:14 +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 4G9nJG6FYlz4sxr; Thu, 24 Jun 2021 17:32:14 +0000 (UTC) (envelope-from git@FreeBSD.org) 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 BE1F91C13A; Thu, 24 Jun 2021 17:32:14 +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 15OHWEpX072292; Thu, 24 Jun 2021 17:32:14 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 15OHWETG072291; Thu, 24 Jun 2021 17:32:14 GMT (envelope-from git) Date: Thu, 24 Jun 2021 17:32:14 GMT Message-Id: <202106241732.15OHWETG072291@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: cf14bbb325bb - main - biology/mmseqs2: Ultra fast and sensitive sequence search and clustering suite 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: cf14bbb325bb8696c275ebbabff3da95a75815eb Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-all@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commit messages for all branches of the ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 24 Jun 2021 17:32:15 -0000 The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=cf14bbb325bb8696c275ebbabff3da95a75815eb commit cf14bbb325bb8696c275ebbabff3da95a75815eb Author: Jason W. Bacon AuthorDate: 2021-06-24 17:29:51 +0000 Commit: Jason W. Bacon CommitDate: 2021-06-24 17:31:42 +0000 biology/mmseqs2: Ultra fast and sensitive sequence search and clustering suite MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for FreeBSD, Linux, MacOS, and (via via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed. --- biology/Makefile | 1 + biology/mmseqs2/Makefile | 27 +++++++++++++++ biology/mmseqs2/distinfo | 3 ++ biology/mmseqs2/files/patch-CMakeLists.txt | 53 ++++++++++++++++++++++++++++++ biology/mmseqs2/pkg-descr | 10 ++++++ 5 files changed, 94 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 158eb70ede1a..55ed6b8c2735 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -77,6 +77,7 @@ SUBDIR += mapm3 SUBDIR += migrate SUBDIR += minimap2 + SUBDIR += mmseqs2 SUBDIR += molden SUBDIR += mopac SUBDIR += mothur diff --git a/biology/mmseqs2/Makefile b/biology/mmseqs2/Makefile new file mode 100644 index 000000000000..6ec07e428c72 --- /dev/null +++ b/biology/mmseqs2/Makefile @@ -0,0 +1,27 @@ +PORTNAME= MMseqs2 +DISTVERSION= 13-45111 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Ultra fast and sensitive sequence search and clustering suite + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE.md + +USES= cmake perl5 shebangfix + +SHEBANG_GLOB= *.sh + +USE_GITHUB= yes +GH_ACCOUNT= soedinglab + +PLIST_FILES= bin/mmseqs ${DATADIR}/bash-completion.sh + +post-patch: + @${REINPLACE_CMD} -e 's|MMSEQS_HOME/util|${DATADIR}|g' \ + ${WRKSRC}/src/commons/Application.cpp + +post-stage: + ${MV} ${STAGEDIR}${PREFIX}/util ${STAGEDIR}${DATADIR} + +.include diff --git a/biology/mmseqs2/distinfo b/biology/mmseqs2/distinfo new file mode 100644 index 000000000000..ec7fbc69cf89 --- /dev/null +++ b/biology/mmseqs2/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1624543564 +SHA256 (soedinglab-MMseqs2-13-45111_GH0.tar.gz) = 6444bb682ebf5ced54b2eda7a301fa3e933c2a28b7661f96ef5bdab1d53695a2 +SIZE (soedinglab-MMseqs2-13-45111_GH0.tar.gz) = 10196433 diff --git a/biology/mmseqs2/files/patch-CMakeLists.txt b/biology/mmseqs2/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..908984972649 --- /dev/null +++ b/biology/mmseqs2/files/patch-CMakeLists.txt @@ -0,0 +1,53 @@ +--- CMakeLists.txt.orig 2021-06-24 14:37:49 UTC ++++ CMakeLists.txt +@@ -50,30 +50,19 @@ set(MMSEQS_CXX_FLAGS "-fsigned-char") + # SIMD instruction sets support + set(MMSEQS_ARCH "") + if (HAVE_AVX2) +- if (CMAKE_COMPILER_IS_CLANG) +- set(MMSEQS_ARCH "${MMSEQS_ARCH} -mavx2 -mcx16") +- else () +- set(MMSEQS_ARCH "${MMSEQS_ARCH} -mavx2 -mcx16 -Wa,-q") +- endif () + set(X64 1) + elseif (HAVE_SSE4_1) +- set(MMSEQS_ARCH "${MMSEQS_ARCH} -msse4.1 -mcx16") + set(X64 1) + elseif (HAVE_SSE2) +- set(MMSEQS_ARCH "${MMSEQS_ARCH} -msse2") + set(DISABLE_IPS4O 1) + set(X64 1) + elseif (HAVE_POWER9) +- set(MMSEQS_ARCH "${MMSEQS_ARCH} -mcpu=power9 -mvsx") + set(PPC64 1) + elseif (HAVE_POWER8) +- set(MMSEQS_ARCH "${MMSEQS_ARCH} -mcpu=power8 -mvsx") + set(PPC64 1) + elseif (HAVE_ARM8) +- set(MMSEQS_ARCH "${MMSEQS_ARCH} -march=armv8-a+simd") + set(ARM 1) + elseif (HAVE_S390X) +- set(MMSEQS_ARCH "${MMSEQS_ARCH} -mzarch -march=z14") + set(ZARCH 1) + endif () + +@@ -105,19 +94,6 @@ if (NATIVE_ARCH AND (MMSEQS_ARCH STREQUAL "")) + endif () + if (PPC64) + set(MMSEQS_ARCH "-mcpu=native") +- else () +- # clang has a problem with march=native on travis +- if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS "4.0.0") +- set(MMSEQS_ARCH "${SSE_FLAGS}") +- else() +- set(MMSEQS_ARCH "-march=native") +- endif() +- endif () +- else () +- if (PPC64) +- set(MMSEQS_ARCH "-mcpu=native") +- else () +- set(MMSEQS_ARCH "-march=native") + endif () + endif () + endif () diff --git a/biology/mmseqs2/pkg-descr b/biology/mmseqs2/pkg-descr new file mode 100644 index 000000000000..128056f15f39 --- /dev/null +++ b/biology/mmseqs2/pkg-descr @@ -0,0 +1,10 @@ +MMseqs2 (Many-against-Many sequence searching) is a software suite to search +and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source +GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta +version, via cygwin) Windows. The software is designed to run on multiple cores +and servers and exhibits very good scalability. MMseqs2 can run 10000 times +faster than BLAST. At 100 times its speed it achieves almost the same +sensitivity. It can perform profile searches with the same sensitivity as +PSI-BLAST at over 400 times its speed. + +WWW: https://github.com/soedinglab/MMseqs2