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

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/