ports/171918: New port: biology/plink
Jason Bacon
jwbacon at tds.net
Mon Sep 24 13:30:10 UTC 2012
>Number: 171918
>Category: ports
>Synopsis: New port: biology/plink
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: change-request
>Submitter-Id: current-users
>Arrival-Date: Mon Sep 24 13:30:09 UTC 2012
>Closed-Date:
>Last-Modified:
>Originator: Jason Bacon
>Release: 9.0-RELEASE
>Organization:
Acadix Consulting, LLC
>Environment:
FreeBSD sculpin.jbacon.dyndns.org 9.0-RELEASE FreeBSD 9.0-RELEASE #0: Tue Jan 3 07:46:30 UTC 2012 root at farrell.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC amd64
>Description:
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.
>How-To-Repeat:
>Fix:
Patch attached with submission follows:
# This is a shell archive. Save it in a file, remove anything before
# this line, and then unpack it by entering "sh file". Note, it may
# create directories; files and directories will be owned by you and
# have default permissions.
#
# This archive contains:
#
# plink
# plink/pkg-descr
# plink/Makefile
# plink/distinfo
# plink/files
# plink/files/patch-Makefile
#
echo c - plink
mkdir -p plink > /dev/null 2>&1
echo x - plink/pkg-descr
sed 's/^X//' >plink/pkg-descr << '13db0b698fc1987e35a2140396ca451a'
XPLINK is a free, open-source whole genome association analysis toolset,
Xdesigned to perform a range of basic, large-scale analyses in a
Xcomputationally efficient manner.
X
XWWW: http://pngu.mgh.harvard.edu/~purcell/plink/
13db0b698fc1987e35a2140396ca451a
echo x - plink/Makefile
sed 's/^X//' >plink/Makefile << '3225f885242ffc903c9410142479cfcd'
X# New ports collection makefile for: plink
X# Date created: 06 September 2012
X# Whom: Jason Bacon <jwbacon at tds.net>
X#
X# $FreeBSD$
X#
X
XPORTNAME= plink
XPORTVERSION= 1.07
XCATEGORIES= biology science
XMASTER_SITES= http://pngu.mgh.harvard.edu/~purcell/plink/dist/
XDISTNAME= ${PORTNAME}-${PORTVERSION}-src
X
XMAINTAINER= jwbacon at tds.net
XCOMMENT= Whole genome association analysis toolset
X
XLICENSE= GPLv2
X
XLIB_DEPENDS= lapack:${PORTSDIR}/math/lapack
X
XUSE_ZIP= yes
XUSE_GMAKE= yes
XUSE_FORTRAN= yes # Make it use the same compiler as lapack
X
XPLIST_FILES= bin/plink
X
Xdo-install:
X ${MKDIR} ${PREFIX}/bin
X ${INSTALL_PROGRAM} ${WRKSRC}/plink ${PREFIX}/bin
X
X.include <bsd.port.mk>
3225f885242ffc903c9410142479cfcd
echo x - plink/distinfo
sed 's/^X//' >plink/distinfo << 'a7e532cb61dd2baca4095cee307ed431'
XSHA256 (plink-1.07-src.zip) = 4af56348443d0c6a1db64950a071b1fcb49cc74154875a7b43cccb4b6a7f482b
XSIZE (plink-1.07-src.zip) = 2257297
a7e532cb61dd2baca4095cee307ed431
echo c - plink/files
mkdir -p plink/files > /dev/null 2>&1
echo x - plink/files/patch-Makefile
sed 's/^X//' >plink/files/patch-Makefile << 'b45708355594ed1e96bc7248f5f1076c'
X--- Makefile.orig 2009-10-10 11:00:20.000000000 -0500
X+++ Makefile 2012-09-07 08:24:26.000000000 -0500
X@@ -26,7 +26,7 @@
X WITH_WEBCHECK = 1
X FORCE_32BIT =
X WITH_ZLIB = 1
X-WITH_LAPACK =
X+WITH_LAPACK = 1
X FORCE_DYNAMIC =
X
X # Put C++ compiler here; Windows has it's own specific version
X@@ -34,17 +34,17 @@
X CXX_WIN = c:\bin\mingw\bin\mingw32-g++.exe
X
X # Any other compiler flags here ( -Wall, -g, etc)
X-CXXFLAGS =
X+# CXXFLAGS =
X
X # Misc
X-LIB_LAPACK = /usr/lib/liblapack.so.3
X+LIB_LAPACK = -L${LOCALBASE}/lib -llapack -lblas -lgfortran
X
X
X # --------------------------------------------------------------------
X # Do not edit below this line
X # --------------------------------------------------------------------
X
X-CXXFLAGS += -O3 -I.
X+CXXFLAGS += -I.
X OUTPUT = plink
X
X # Some system specific flags
X@@ -58,8 +58,8 @@
X endif
X
X ifeq ($(SYS),UNIX)
X- CXXFLAGS += -DUNIX
X- CXX = $(CXX_UNIX)
X+ CXXFLAGS += -DUNIX -Dfopen64=fopen
X+ CXX ?= $(CXX_UNIX)
X ifndef FORCE_DYNAMIC
X CXXFLAGS += -static
X endif
X@@ -128,7 +128,7 @@
X LIB += -ldl
X endif
X ifeq ($(SYS),UNIX)
X-LIB += -ldl -lcrypt
X+LIB += -lcrypt
X endif
X endif
X
b45708355594ed1e96bc7248f5f1076c
exit
>Release-Note:
>Audit-Trail:
>Unformatted:
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