979be07cda
From Jason Bacon via pkgsrc-wip. 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.
76 lines
1.7 KiB
Text
76 lines
1.7 KiB
Text
$NetBSD: patch-Makefile,v 1.1.1.1 2012/09/14 17:46:23 asau Exp $
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--- Makefile.orig 2009-10-10 16:00:20.000000000 +0000
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+++ Makefile
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@@ -19,32 +19,32 @@
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# ---------------------------------------------------------------------
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# Set this variable to either UNIX, MAC or WIN
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-SYS = UNIX
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+SYS ?= UNIX
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# Leave blank after "=" to disable; put "= 1" to enable
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WITH_R_PLUGINS = 1
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WITH_WEBCHECK = 1
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-FORCE_32BIT =
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+FORCE_32BIT ?=
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WITH_ZLIB = 1
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-WITH_LAPACK =
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-FORCE_DYNAMIC =
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+WITH_LAPACK ?=
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+FORCE_DYNAMIC ?=
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# Put C++ compiler here; Windows has it's own specific version
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CXX_UNIX = g++
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CXX_WIN = c:\bin\mingw\bin\mingw32-g++.exe
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# Any other compiler flags here ( -Wall, -g, etc)
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-CXXFLAGS =
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+CXXFLAGS ?=
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# Misc
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-LIB_LAPACK = /usr/lib/liblapack.so.3
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-
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+LIB_LAPACK ?= /usr/lib/liblapack.so.3
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+LIBDL ?= -ldl
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# --------------------------------------------------------------------
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# Do not edit below this line
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# --------------------------------------------------------------------
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-CXXFLAGS += -O3 -I.
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+CXXFLAGS += -I.
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OUTPUT = plink
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# Some system specific flags
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@@ -59,7 +59,7 @@ endif
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ifeq ($(SYS),UNIX)
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CXXFLAGS += -DUNIX
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- CXX = $(CXX_UNIX)
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+ CXX ?= $(CXX_UNIX)
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ifndef FORCE_DYNAMIC
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CXXFLAGS += -static
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endif
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@@ -125,10 +125,10 @@ CXXFLAGS += -DWITH_R_PLUGINS
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HDR += sisocks.h Rsrv.h Rconnection.h config.h
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SRC += r.cpp Rconnection.cpp
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ifeq ($(SYS),MAC)
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-LIB += -ldl
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+LIB += ${LIBDL}
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endif
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ifeq ($(SYS),UNIX)
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-LIB += -ldl -lcrypt
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+LIB += ${LIBDL} -lcrypt
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endif
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endif
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@@ -151,7 +151,7 @@ OBJ = $(SRC:.cpp=.o)
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all : $(OUTPUT)
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$(OUTPUT) :
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- $(CXX) $(CXXFLAGS) -o $(OUTPUT) $(OBJ) $(LIB)
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+ $(CXX) -o $(OUTPUT) $(OBJ) $(LIB)
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$(OBJ) : $(HDR)
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