diff options
author | Wen Heping <wen@FreeBSD.org> | 2016-05-06 08:45:02 +0000 |
---|---|---|
committer | Wen Heping <wen@FreeBSD.org> | 2016-05-06 08:45:02 +0000 |
commit | ec07b546cf7c736ad2c1ded03fcff9ca30caed85 (patch) | |
tree | 1d6cf1d8d7999cd68373c0a445faa6779f8f5552 /biology | |
parent | - Update to 2.2.2 (diff) |
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
Notes
Notes:
svn path=/head/; revision=414686
Diffstat (limited to 'biology')
-rw-r--r-- | biology/Makefile | 1 | ||||
-rw-r--r-- | biology/diamond/Makefile | 28 | ||||
-rw-r--r-- | biology/diamond/distinfo | 2 | ||||
-rw-r--r-- | biology/diamond/files/patch-CMakeLists.txt | 33 | ||||
-rw-r--r-- | biology/diamond/pkg-descr | 7 |
5 files changed, 71 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 89b081a81358..d8ff8900e298 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -21,6 +21,7 @@ SUBDIR += clustalw SUBDIR += consed SUBDIR += crux + SUBDIR += diamond SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 diff --git a/biology/diamond/Makefile b/biology/diamond/Makefile new file mode 100644 index 000000000000..bd0a5d48806a --- /dev/null +++ b/biology/diamond/Makefile @@ -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= ${LOCALBASE}/include/boost:devel/boost-libs + +ONLY_FOR_ARCHS= amd64 + +USES= cmake:outsource + +CFLAGS+= -DNDEBUG + +USE_GITHUB= yes +GH_ACCOUNT= bbuchfink + +PLIST_FILES= bin/diamond + +.include <bsd.port.mk> diff --git a/biology/diamond/distinfo b/biology/diamond/distinfo new file mode 100644 index 000000000000..9fc724f22800 --- /dev/null +++ b/biology/diamond/distinfo @@ -0,0 +1,2 @@ +SHA256 (bbuchfink-diamond-v0.7.12_GH0.tar.gz) = 16f8f618e4e5e81071ef8b66dc39685a1e969434ddeff3d88fa01091971b662f +SIZE (bbuchfink-diamond-v0.7.12_GH0.tar.gz) = 1826614 diff --git a/biology/diamond/files/patch-CMakeLists.txt b/biology/diamond/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..167cf967e353 --- /dev/null +++ b/biology/diamond/files/patch-CMakeLists.txt @@ -0,0 +1,33 @@ +--- CMakeLists.txt.orig 2016-03-29 09:23:52 UTC ++++ CMakeLists.txt +@@ -9,6 +9,7 @@ if(BUILD_STATIC) + set(CMAKE_EXE_LINKER_FLAGS "-static") + endif() + ++FIND_PACKAGE(Threads REQUIRED) + find_package(Boost + 1.53.0 REQUIRED + COMPONENTS program_options timer iostreams thread +@@ -16,9 +17,6 @@ find_package(Boost + + find_package(ZLIB REQUIRED) + +-set(CMAKE_BUILD_TYPE Release) +-set(CMAKE_CXX_FLAGS "${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() diff --git a/biology/diamond/pkg-descr b/biology/diamond/pkg-descr new file mode 100644 index 000000000000..c625bbcdf61e --- /dev/null +++ b/biology/diamond/pkg-descr @@ -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/ |