From owner-svn-ports-head@freebsd.org Sun May 19 06:52:41 2019 Return-Path: Delivered-To: svn-ports-head@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 740E115A5076; Sun, 19 May 2019 06:52:41 +0000 (UTC) (envelope-from yuri@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) server-signature RSA-PSS (4096 bits) client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 189B282339; Sun, 19 May 2019 06:52:41 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id E563F37E7; Sun, 19 May 2019 06:52:40 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id x4J6qeUh063733; Sun, 19 May 2019 06:52:40 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id x4J6qdCk063725; Sun, 19 May 2019 06:52:39 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <201905190652.x4J6qdCk063725@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Sun, 19 May 2019 06:52:39 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r502015 - in head/biology: . hhsuite hhsuite/files X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: in head/biology: . hhsuite hhsuite/files X-SVN-Commit-Revision: 502015 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: 189B282339 X-Spamd-Bar: -- Authentication-Results: mx1.freebsd.org X-Spamd-Result: default: False [-2.98 / 15.00]; local_wl_from(0.00)[FreeBSD.org]; NEURAL_HAM_MEDIUM(-1.00)[-0.999,0]; NEURAL_HAM_LONG(-1.00)[-1.000,0]; NEURAL_HAM_SHORT(-0.98)[-0.984,0]; ASN(0.00)[asn:11403, ipnet:2610:1c1:1::/48, country:US] X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 19 May 2019 06:52:41 -0000 Author: yuri Date: Sun May 19 06:52:38 2019 New Revision: 502015 URL: https://svnweb.freebsd.org/changeset/ports/502015 Log: New port: biology/hhsuite: Remote protein homology detection suite Added: head/biology/hhsuite/ head/biology/hhsuite/Makefile (contents, props changed) head/biology/hhsuite/distinfo (contents, props changed) head/biology/hhsuite/files/ head/biology/hhsuite/files/patch-data_CMakeLists.txt (contents, props changed) head/biology/hhsuite/files/patch-scripts_CMakeLists.txt (contents, props changed) head/biology/hhsuite/files/patch-src_cs_getopt__pp.cc (contents, props changed) head/biology/hhsuite/pkg-descr (contents, props changed) head/biology/hhsuite/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Sun May 19 06:08:58 2019 (r502014) +++ head/biology/Makefile Sun May 19 06:52:38 2019 (r502015) @@ -49,6 +49,7 @@ SUBDIR += graphlan SUBDIR += grappa SUBDIR += groopm + SUBDIR += hhsuite SUBDIR += hisat2 SUBDIR += hmmer SUBDIR += htslib Added: head/biology/hhsuite/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/hhsuite/Makefile Sun May 19 06:52:38 2019 (r502015) @@ -0,0 +1,26 @@ +# $FreeBSD$ + +PORTNAME= hhsuite +DISTVERSIONPREFIX= v +DISTVERSION= 3.2.0 +CATEGORIES= biology science + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Remote protein homology detection suite + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= openmpi>0:net/openmpi +LIB_DEPENDS= libomp.so:devel/openmp +RUN_DEPENDS= openmpi>0:net/openmpi + +USES= cmake perl5 python shebangfix +SHEBANG_GLOB= *.pl *.py +USE_GITHUB= yes +GH_ACCOUNT= soedinglab +GH_PROJECT= hh-suite + +LDFLAGS+= -Wl,-rpath,${LOCALBASE}/mpi/openmpi/lib -L${LOCALBASE}/mpi/openmpi/lib -lmpi # force linking to openmpi, and not to mpich + +.include Added: head/biology/hhsuite/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/hhsuite/distinfo Sun May 19 06:52:38 2019 (r502015) @@ -0,0 +1,3 @@ +TIMESTAMP = 1558244086 +SHA256 (soedinglab-hh-suite-v3.2.0_GH0.tar.gz) = 6b870dcfbc1ffb9dd664a45415fcd13cf5970f49d1c7b824160c260fa138e6d6 +SIZE (soedinglab-hh-suite-v3.2.0_GH0.tar.gz) = 6273589 Added: head/biology/hhsuite/files/patch-data_CMakeLists.txt ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/hhsuite/files/patch-data_CMakeLists.txt Sun May 19 06:52:38 2019 (r502015) @@ -0,0 +1,11 @@ +--- data/CMakeLists.txt.orig 2019-05-19 05:46:02 UTC ++++ data/CMakeLists.txt +@@ -7,7 +7,7 @@ INSTALL(FILES + do_not_delete.pin + do_not_delete.psq + PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ +- DESTINATION data ++ DESTINATION ${CMAKE_INSTALL_PREFIX}/share/hhsuite/data + ) + + include(ResourceCompiler) Added: head/biology/hhsuite/files/patch-scripts_CMakeLists.txt ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/hhsuite/files/patch-scripts_CMakeLists.txt Sun May 19 06:52:38 2019 (r502015) @@ -0,0 +1,9 @@ +--- scripts/CMakeLists.txt.orig 2019-05-19 05:44:58 UTC ++++ scripts/CMakeLists.txt +@@ -21,5 +21,5 @@ INSTALL(PROGRAMS + reformat.pl + renumberpdb.pl + splitfasta.pl +- DESTINATION scripts ++ DESTINATION ${CMAKE_INSTALL_PREFIX}/share/hhsuite/scripts + ) Added: head/biology/hhsuite/files/patch-src_cs_getopt__pp.cc ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/hhsuite/files/patch-src_cs_getopt__pp.cc Sun May 19 06:52:38 2019 (r502015) @@ -0,0 +1,11 @@ +--- src/cs/getopt_pp.cc.orig 2019-05-19 05:36:03 UTC ++++ src/cs/getopt_pp.cc +@@ -21,7 +21,7 @@ + #include + #include "getopt_pp.h" + +-#ifdef __APPLE__ ++#if defined(__APPLE__) || defined(__FreeBSD__) + extern char** environ; + #endif + Added: head/biology/hhsuite/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/hhsuite/pkg-descr Sun May 19 06:52:38 2019 (r502015) @@ -0,0 +1,8 @@ +SIMD-vectorized implementation of the Viterbi algorithm for profile HMM +alignment and introduced various other speed-ups. This accelerated HHsearch by a +factor 4 and HHblits by a factor 2 over the previous version 2.0.16. HHblits3 is +~10x faster than PSI-BLAST and ~20x faster than HMMER3. Jobs to perform HHsearch +and HHblits searches with many query profile HMMs can be parallelized over cores +and over servers in a cluster using OpenMP and message passing interface (MPI). + +WWW: https://github.com/soedinglab/hh-suite Added: head/biology/hhsuite/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/hhsuite/pkg-plist Sun May 19 06:52:38 2019 (r502015) @@ -0,0 +1,59 @@ +bin/a3m_database_extract +bin/a3m_database_filter +bin/a3m_database_reduce +bin/a3m_extract +bin/a3m_reduce +bin/cstranslate +bin/cstranslate_mpi +bin/ffindex_apply +bin/ffindex_apply_mpi +bin/ffindex_build +bin/ffindex_from_fasta +bin/ffindex_from_fasta_with_split +bin/ffindex_get +bin/ffindex_modify +bin/ffindex_order +bin/ffindex_reduce +bin/ffindex_unpack +bin/hhalign +bin/hhalign_mpi +bin/hhalign_omp +bin/hhblits +bin/hhblits_ca3m +bin/hhblits_mpi +bin/hhblits_omp +bin/hhconsensus +bin/hhfilter +bin/hhmake +bin/hhsearch +bin/hhsearch_mpi +bin/hhsearch_omp +%%DATADIR%%/data/context_data.crf +%%DATADIR%%/data/context_data.lib +%%DATADIR%%/data/cs219.lib +%%DATADIR%%/data/do_not_delete +%%DATADIR%%/data/do_not_delete.phr +%%DATADIR%%/data/do_not_delete.pin +%%DATADIR%%/data/do_not_delete.psq +%%DATADIR%%/scripts/Align.pm +%%DATADIR%%/scripts/HHPaths.pm +%%DATADIR%%/scripts/a3m.py +%%DATADIR%%/scripts/addss.pl +%%DATADIR%%/scripts/check_a3m.py +%%DATADIR%%/scripts/cif2fasta.py +%%DATADIR%%/scripts/create_profile_from_hhm.pl +%%DATADIR%%/scripts/create_profile_from_hmmer.pl +%%DATADIR%%/scripts/ffindex.py +%%DATADIR%%/scripts/get_a3m_size.py +%%DATADIR%%/scripts/hh_reader.py +%%DATADIR%%/scripts/hhmakemodel.pl +%%DATADIR%%/scripts/hhmakemodel.py +%%DATADIR%%/scripts/hhsuitedb.py +%%DATADIR%%/scripts/mergeali.pl +%%DATADIR%%/scripts/multithread.pl +%%DATADIR%%/scripts/pdb2fasta.pl +%%DATADIR%%/scripts/pdbfilter.pl +%%DATADIR%%/scripts/pdbfilter.py +%%DATADIR%%/scripts/reformat.pl +%%DATADIR%%/scripts/renumberpdb.pl +%%DATADIR%%/scripts/splitfasta.pl