Date: Fri, 6 May 2016 08:45:02 +0000 (UTC) From: Wen Heping <wen@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r414686 - in head/biology: . diamond diamond/files Message-ID: <201605060845.u468j2mJ081327@repo.freebsd.org>
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Author: wen Date: Fri May 6 08:45:02 2016 New Revision: 414686 URL: https://svnweb.freebsd.org/changeset/ports/414686 Log: DNA query sequences against a protein reference database (BLASTP and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short reads at a typical sensitivity of 90-99% relative to BLAST depending on the data and settings. WWW: http://ab.inf.uni-tuebingen.de/software/diamond/ PR: 208998 Submitted by: jrm@ftfl.ca Added: head/biology/diamond/ head/biology/diamond/Makefile (contents, props changed) head/biology/diamond/distinfo (contents, props changed) head/biology/diamond/files/ head/biology/diamond/files/patch-CMakeLists.txt (contents, props changed) head/biology/diamond/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Fri May 6 08:11:26 2016 (r414685) +++ head/biology/Makefile Fri May 6 08:45:02 2016 (r414686) @@ -21,6 +21,7 @@ SUBDIR += clustalw SUBDIR += consed SUBDIR += crux + SUBDIR += diamond SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 Added: head/biology/diamond/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/diamond/Makefile Fri May 6 08:45:02 2016 (r414686) @@ -0,0 +1,28 @@ +# Created by: jrm@ftfl.ca +# $FreeBSD$ + +PORTNAME= diamond +PORTVERSION= 0.7.12 +DISTVERSIONPREFIX= v +CATEGORIES= biology + +MAINTAINER= jrm@ftfl.ca +COMMENT= BLAST-compatible local sequence aligner + +LICENSE= BSD2CLAUSE + +BUILD_DEPENDS= ${LOCALBASE}/include/boost:devel/boost-libs +RUN_DEPENDS= ${LOCALBASE}/include/boost:devel/boost-libs + +ONLY_FOR_ARCHS= amd64 + +USES= cmake:outsource + +CFLAGS+= -DNDEBUG + +USE_GITHUB= yes +GH_ACCOUNT= bbuchfink + +PLIST_FILES= bin/diamond + +.include <bsd.port.mk> Added: head/biology/diamond/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/diamond/distinfo Fri May 6 08:45:02 2016 (r414686) @@ -0,0 +1,2 @@ +SHA256 (bbuchfink-diamond-v0.7.12_GH0.tar.gz) = 16f8f618e4e5e81071ef8b66dc39685a1e969434ddeff3d88fa01091971b662f +SIZE (bbuchfink-diamond-v0.7.12_GH0.tar.gz) = 1826614 Added: head/biology/diamond/files/patch-CMakeLists.txt ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/diamond/files/patch-CMakeLists.txt Fri May 6 08:45:02 2016 (r414686) @@ -0,0 +1,33 @@ +--- CMakeLists.txt.orig 2016-03-29 09:23:52 UTC ++++ CMakeLists.txt +@@ -9,6 +9,7 @@ if(BUILD_STATIC) + set(CMAKE_EXE_LINKER_FLAGS "-static") + endif() + ++FIND_PACKAGE(Threads REQUIRED) + find_package(Boost + 1.53.0 REQUIRED + COMPONENTS program_options timer iostreams thread +@@ -16,9 +17,6 @@ find_package(Boost + + find_package(ZLIB REQUIRED) + +-set(CMAKE_BUILD_TYPE Release) +-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wno-uninitialized") +- + add_subdirectory("src/algo/blast/core") + include_directories( + "${CMAKE_SOURCE_DIR}/src" +@@ -29,6 +27,11 @@ add_executable(diamond src/main.cpp + src/basic/options.cpp + src/util/tinythread.cpp) + +-target_link_libraries(diamond blast_core ${Boost_LIBRARIES} ${ZLIB_LIBRARY}) ++target_link_libraries(diamond blast_core ${Boost_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} ${ZLIB_LIBRARY}) + + install(TARGETS diamond DESTINATION bin) ++ ++get_cmake_property(_variableNames VARIABLES) ++foreach (_variableName ${_variableNames}) ++ message(STATUS "${_variableName}=${${_variableName}}") ++endforeach() Added: head/biology/diamond/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/diamond/pkg-descr Fri May 6 08:45:02 2016 (r414686) @@ -0,0 +1,7 @@ +DIAMOND is a BLAST-compatible local aligner for mapping protein and translated +DNA query sequences against a protein reference database (BLASTP and BLASTX +alignment mode). The speedup over BLAST is up to 20,000 on short reads at a +typical sensitivity of 90-99% relative to BLAST depending on the data and +settings. + +WWW: http://ab.inf.uni-tuebingen.de/software/diamond/
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