Import PLINK 1.07 as biology/plink

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.

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)
+