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authorasau <asau@pkgsrc.org>2012-09-14 17:46:23 +0000
committerasau <asau@pkgsrc.org>2012-09-14 17:46:23 +0000
commit4a393e76dd497a816f17f8e1421aacb28ea1ae28 (patch)
treef7075a3661029a1d431531bdf4229e03de97e20b /biology/plink
parente671549e23688c69865f9445a14212abdb357e72 (diff)
downloadpkgsrc-4a393e76dd497a816f17f8e1421aacb28ea1ae28.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.
Diffstat (limited to 'biology/plink')
-rw-r--r--biology/plink/DESCR10
-rw-r--r--biology/plink/DESCR.~1.2.~1
-rw-r--r--biology/plink/Makefile39
-rw-r--r--biology/plink/PLIST2
-rw-r--r--biology/plink/distinfo6
-rw-r--r--biology/plink/patches/patch-Makefile76
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)
+