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author | asau <asau> | 2012-09-14 17:46:23 +0000 |
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committer | asau <asau> | 2012-09-14 17:46:23 +0000 |
commit | 76a47736e9170a356a2fa9bb524468b58e7bc8ae (patch) | |
tree | f7075a3661029a1d431531bdf4229e03de97e20b | |
parent | eab09553ff1fcb184daa9e0dc599d28919843f19 (diff) | |
download | pkgsrc-76a47736e9170a356a2fa9bb524468b58e7bc8ae.tar.gz |
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.
-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) + |