From 4a393e76dd497a816f17f8e1421aacb28ea1ae28 Mon Sep 17 00:00:00 2001 From: asau Date: Fri, 14 Sep 2012 17:46:23 +0000 Subject: 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. --- biology/plink/DESCR | 10 +++++ biology/plink/DESCR.~1.2.~ | 1 + biology/plink/Makefile | 39 ++++++++++++++++++ biology/plink/PLIST | 2 + biology/plink/distinfo | 6 +++ biology/plink/patches/patch-Makefile | 76 ++++++++++++++++++++++++++++++++++++ 6 files changed, 134 insertions(+) create mode 100644 biology/plink/DESCR create mode 100644 biology/plink/DESCR.~1.2.~ create mode 100644 biology/plink/Makefile create mode 100644 biology/plink/PLIST create mode 100644 biology/plink/distinfo create mode 100644 biology/plink/patches/patch-Makefile 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) + -- cgit v1.2.3