diff options
| -rw-r--r-- | biology/plink/DESCR | 10 | ||||
| -rw-r--r-- | biology/plink/DESCR.~1.2.~ | 1 | ||||
| -rw-r--r-- | biology/plink/Makefile | 39 | ||||
| -rw-r--r-- | biology/plink/PLIST | 2 | ||||
| -rw-r--r-- | biology/plink/distinfo | 6 | ||||
| -rw-r--r-- | biology/plink/patches/patch-Makefile | 76 |
6 files changed, 134 insertions, 0 deletions
diff --git a/biology/plink/DESCR b/biology/plink/DESCR new file mode 100644 index 00000000000..d5e27edb64a --- /dev/null +++ b/biology/plink/DESCR @@ -0,0 +1,10 @@ +PLINK is a free, open-source whole genome association analysis +toolset, designed to perform a range of basic, large-scale +analyses in a computationally efficient manner. + +The focus of PLINK is purely on analysis of genotype/phenotype +data, so there is no support for steps prior to this (e.g. study +design and planning, generating genotype or CNV calls from raw +data). Through integration with gPLINK and Haploview, there is +some support for the subsequent visualization, annotation and +storage of results. diff --git a/biology/plink/DESCR.~1.2.~ b/biology/plink/DESCR.~1.2.~ new file mode 100644 index 00000000000..7b005619b52 --- /dev/null +++ b/biology/plink/DESCR.~1.2.~ @@ -0,0 +1 @@ +Whole-genome association analysis toolset. diff --git a/biology/plink/Makefile b/biology/plink/Makefile new file mode 100644 index 00000000000..af83a88a80d --- /dev/null +++ b/biology/plink/Makefile @@ -0,0 +1,39 @@ +# $NetBSD: Makefile,v 1.1.1.1 2012/09/14 17:46:23 asau Exp $ + +DISTNAME= plink-1.07-src +CATEGORIES= biology +MASTER_SITES= http://pngu.mgh.harvard.edu/~purcell/plink/dist/ +EXTRACT_SUFX= .zip + +MAINTAINER= jwbacon@tds.net +HOMEPAGE= http://pngu.mgh.harvard.edu/~purcell/plink/ +COMMENT= Whole-genome association analysis toolset +LICENSE= gnu-gpl-v2 + +USE_LANGUAGES= c c++ fortran77 +USE_TOOLS+= gmake + +CXXFLAGS+= -Dfopen64=fopen + +MAKE_FLAGS+= LIBDL=${DL_LIBS:Q} + +LIB_LAPACK= -L${LOCALBASE}/lib ${COMPILER_RPATH_FLAG}${LOCALBASE}/lib -llapack -lblas -lf2c +MAKE_FLAGS+= WITH_LAPACK=1 LIB_LAPACK=${LIB_LAPACK:Q} + +INSTALLATION_DIRS= bin + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/plink ${DESTDIR}${PREFIX}/bin + +do-test: + cd $(WRKSRC) && ./plink --file test + cd $(WRKSRC) && ./plink --file test --freq + cd $(WRKSRC) && ./plink --file test --assoc + cd $(WRKSRC) && ./plink --file test --make-bed + +.include "../../devel/libf2c/buildlink3.mk" +.include "../../devel/zlib/buildlink3.mk" +.include "../../math/lapack/buildlink3.mk" +.include "../../math/blas/buildlink3.mk" +.include "../../mk/dlopen.buildlink3.mk" +.include "../../mk/bsd.pkg.mk" diff --git a/biology/plink/PLIST b/biology/plink/PLIST new file mode 100644 index 00000000000..7da2bc98a44 --- /dev/null +++ b/biology/plink/PLIST @@ -0,0 +1,2 @@ +@comment $NetBSD: PLIST,v 1.1.1.1 2012/09/14 17:46:23 asau Exp $ +bin/plink diff --git a/biology/plink/distinfo b/biology/plink/distinfo new file mode 100644 index 00000000000..cbe6e2c93d5 --- /dev/null +++ b/biology/plink/distinfo @@ -0,0 +1,6 @@ +$NetBSD: distinfo,v 1.1.1.1 2012/09/14 17:46:23 asau Exp $ + +SHA1 (plink-1.07-src.zip) = d41a2d014ebc02bf11e5235292b50fad6dedd407 +RMD160 (plink-1.07-src.zip) = ce22e2388fc711ac9938d21ffd3cb68512ba1150 +Size (plink-1.07-src.zip) = 2257297 bytes +SHA1 (patch-Makefile) = cb01e12cea61d1fe41f352759481277284d9c187 diff --git a/biology/plink/patches/patch-Makefile b/biology/plink/patches/patch-Makefile new file mode 100644 index 00000000000..52b2428e9a2 --- /dev/null +++ b/biology/plink/patches/patch-Makefile @@ -0,0 +1,76 @@ +$NetBSD: patch-Makefile,v 1.1.1.1 2012/09/14 17:46:23 asau Exp $ + +--- Makefile.orig 2009-10-10 16:00:20.000000000 +0000 ++++ Makefile +@@ -19,32 +19,32 @@ + # --------------------------------------------------------------------- + + # Set this variable to either UNIX, MAC or WIN +-SYS = UNIX ++SYS ?= UNIX + + # Leave blank after "=" to disable; put "= 1" to enable + WITH_R_PLUGINS = 1 + WITH_WEBCHECK = 1 +-FORCE_32BIT = ++FORCE_32BIT ?= + WITH_ZLIB = 1 +-WITH_LAPACK = +-FORCE_DYNAMIC = ++WITH_LAPACK ?= ++FORCE_DYNAMIC ?= + + # Put C++ compiler here; Windows has it's own specific version + CXX_UNIX = g++ + CXX_WIN = c:\bin\mingw\bin\mingw32-g++.exe + + # Any other compiler flags here ( -Wall, -g, etc) +-CXXFLAGS = ++CXXFLAGS ?= + + # Misc +-LIB_LAPACK = /usr/lib/liblapack.so.3 +- ++LIB_LAPACK ?= /usr/lib/liblapack.so.3 ++LIBDL ?= -ldl + + # -------------------------------------------------------------------- + # Do not edit below this line + # -------------------------------------------------------------------- + +-CXXFLAGS += -O3 -I. ++CXXFLAGS += -I. + OUTPUT = plink + + # Some system specific flags +@@ -59,7 +59,7 @@ endif + + ifeq ($(SYS),UNIX) + CXXFLAGS += -DUNIX +- CXX = $(CXX_UNIX) ++ CXX ?= $(CXX_UNIX) + ifndef FORCE_DYNAMIC + CXXFLAGS += -static + endif +@@ -125,10 +125,10 @@ CXXFLAGS += -DWITH_R_PLUGINS + HDR += sisocks.h Rsrv.h Rconnection.h config.h + SRC += r.cpp Rconnection.cpp + ifeq ($(SYS),MAC) +-LIB += -ldl ++LIB += ${LIBDL} + endif + ifeq ($(SYS),UNIX) +-LIB += -ldl -lcrypt ++LIB += ${LIBDL} -lcrypt + endif + endif + +@@ -151,7 +151,7 @@ OBJ = $(SRC:.cpp=.o) + all : $(OUTPUT) + + $(OUTPUT) : +- $(CXX) $(CXXFLAGS) -o $(OUTPUT) $(OBJ) $(LIB) ++ $(CXX) -o $(OUTPUT) $(OBJ) $(LIB) + + $(OBJ) : $(HDR) + |