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| author | Max Brazhnikov <makc@FreeBSD.org> | 2012-09-27 09:59:25 +0000 |
|---|---|---|
| committer | Max Brazhnikov <makc@FreeBSD.org> | 2012-09-27 09:59:25 +0000 |
| commit | ecd280d8207b5c7d43c785405a3aff5b7781710c (patch) | |
| tree | 79b7d185429befe9c68006cc1d45ecc88edb7776 /biology/plink | |
| parent | 47ad784422cc954b19911e16ba628e7d2b6db88e (diff) | |
| download | ports-ecd280d8207b5c7d43c785405a3aff5b7781710c.tar.gz ports-ecd280d8207b5c7d43c785405a3aff5b7781710c.zip | |
Add new ports biology/plink [1] and biology/plinkseq [2]:
PLINK is a free, open-source whole genome association analysis toolset.
PLINK/SEQ is an open-source C/C++ library for working with human
genetic variation data.
PR: ports/171918 [1]
PR: ports/171922 [2]
Submitted by: Jason Bacon <jwbacon at tds.net>
Notes
Notes:
svn path=/head/; revision=304954
Diffstat (limited to 'biology/plink')
| -rw-r--r-- | biology/plink/Makefile | 27 | ||||
| -rw-r--r-- | biology/plink/distinfo | 2 | ||||
| -rw-r--r-- | biology/plink/files/patch-Makefile | 52 | ||||
| -rw-r--r-- | biology/plink/pkg-descr | 5 |
4 files changed, 86 insertions, 0 deletions
diff --git a/biology/plink/Makefile b/biology/plink/Makefile new file mode 100644 index 000000000000..3972649775f7 --- /dev/null +++ b/biology/plink/Makefile @@ -0,0 +1,27 @@ +# Created by: Jason Bacon <jwbacon@tds.net> +# $FreeBSD$ + +PORTNAME= plink +PORTVERSION= 1.07 +CATEGORIES= biology science +MASTER_SITES= http://pngu.mgh.harvard.edu/~purcell/plink/dist/ +DISTNAME= ${PORTNAME}-${PORTVERSION}-src + +MAINTAINER= jwbacon@tds.net +COMMENT= Whole genome association analysis toolset + +LICENSE= GPLv2 + +LIB_DEPENDS= lapack:${PORTSDIR}/math/lapack + +USE_ZIP= yes +USE_GMAKE= yes +USE_FORTRAN= yes # Make it use the same compiler as lapack + +PLIST_FILES= bin/plink + +do-install: + ${MKDIR} ${PREFIX}/bin + ${INSTALL_PROGRAM} ${WRKSRC}/plink ${PREFIX}/bin + +.include <bsd.port.mk> diff --git a/biology/plink/distinfo b/biology/plink/distinfo new file mode 100644 index 000000000000..0e6de032e915 --- /dev/null +++ b/biology/plink/distinfo @@ -0,0 +1,2 @@ +SHA256 (plink-1.07-src.zip) = 4af56348443d0c6a1db64950a071b1fcb49cc74154875a7b43cccb4b6a7f482b +SIZE (plink-1.07-src.zip) = 2257297 diff --git a/biology/plink/files/patch-Makefile b/biology/plink/files/patch-Makefile new file mode 100644 index 000000000000..cb1e7f5fc537 --- /dev/null +++ b/biology/plink/files/patch-Makefile @@ -0,0 +1,52 @@ +--- Makefile.orig 2009-10-10 11:00:20.000000000 -0500 ++++ Makefile 2012-09-07 08:24:26.000000000 -0500 +@@ -26,7 +26,7 @@ + WITH_WEBCHECK = 1 + FORCE_32BIT = + WITH_ZLIB = 1 +-WITH_LAPACK = ++WITH_LAPACK = 1 + FORCE_DYNAMIC = + + # Put C++ compiler here; Windows has it's own specific version +@@ -34,17 +34,17 @@ + CXX_WIN = c:\bin\mingw\bin\mingw32-g++.exe + + # Any other compiler flags here ( -Wall, -g, etc) +-CXXFLAGS = ++# CXXFLAGS = + + # Misc +-LIB_LAPACK = /usr/lib/liblapack.so.3 ++LIB_LAPACK = -L${LOCALBASE}/lib -llapack -lblas -lgfortran + + + # -------------------------------------------------------------------- + # Do not edit below this line + # -------------------------------------------------------------------- + +-CXXFLAGS += -O3 -I. ++CXXFLAGS += -I. + OUTPUT = plink + + # Some system specific flags +@@ -58,8 +58,8 @@ + endif + + ifeq ($(SYS),UNIX) +- CXXFLAGS += -DUNIX +- CXX = $(CXX_UNIX) ++ CXXFLAGS += -DUNIX -Dfopen64=fopen ++ CXX ?= $(CXX_UNIX) + ifndef FORCE_DYNAMIC + CXXFLAGS += -static + endif +@@ -128,7 +128,7 @@ + LIB += -ldl + endif + ifeq ($(SYS),UNIX) +-LIB += -ldl -lcrypt ++LIB += -lcrypt + endif + endif + diff --git a/biology/plink/pkg-descr b/biology/plink/pkg-descr new file mode 100644 index 000000000000..cc38aca9112e --- /dev/null +++ b/biology/plink/pkg-descr @@ -0,0 +1,5 @@ +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. + +WWW: http://pngu.mgh.harvard.edu/~purcell/plink/ |