# 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/files
#	plink/files/patch-plink__common.h
#	plink/Makefile
#	plink/pkg-plist
#	plink/distinfo
#
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 widely used toolset for genome-wide association studies (GWAS) and
Xresearch in population genetics.
X
XCitation:
XChang et al. (2015)
XSecond-generation PLINK: rising to the challenge of larger and richer datasets.
XGigaScience 4(1) doi:10.1186/s13742-015-0047-8
X
XWWW: https://www.cog-genomics.org/plink/
13db0b698fc1987e35a2140396ca451a
echo c - plink/files
mkdir -p plink/files > /dev/null 2>&1
echo x - plink/files/patch-plink__common.h
sed 's/^X//' >plink/files/patch-plink__common.h << 'd9ed87deb2e2c367366dde611e36b2ec'
X--- plink_common.h.orig	2020-01-22 01:51:56 UTC
X+++ plink_common.h
X@@ -122,7 +122,7 @@
X   #define EOLN_STR "\n"
X   #define FOPEN_RB "r"
X   #define FOPEN_WB "w"
X-  #ifndef __APPLE__
X+  #if !defined(__APPLE__) && !defined(__FreeBSD__)
X     // argh
X     // not sure what the right threshold actually is, but this works for now
X     // (may break on gcc <3.0?  but that shouldn't matter anymore)
X@@ -143,7 +143,7 @@
X   #define CLZLU __builtin_clzl
X   #ifndef __LP64__
X     // attempt to patch GCC 6 build failure
X-    #if (__GNUC__ <= 4) && (__GNUC_MINOR__ < 8)
X+    #if !defined(__FreeBSD__) && (__GNUC__ <= 4) && (__GNUC_MINOR__ < 8)
X       #ifndef uintptr_t
X         #define uintptr_t unsigned long
X       #endif
d9ed87deb2e2c367366dde611e36b2ec
echo x - plink/Makefile
sed 's/^X//' >plink/Makefile << '3225f885242ffc903c9410142479cfcd'
X# $FreeBSD$
X
XPORTNAME=	plink
XDISTVERSIONPREFIX=	v
XDISTVERSION=	1.90b6.15
XCATEGORIES=	biology
X
XMAINTAINER=	mzaki@e-mail.ne.jp
XCOMMENT=	Whole genome association analysis toolset
X
XLICENSE=	GPLv3
XLICENSE_FILE=	${WRKSRC}/LICENSE
X
XNOT_FOR_ARCHS=	aarch64 mips64 powerpc64 sparc64
XNOT_FOR_ARCHS_REASON=	64bit code requires SSE2 instructions
X
XUSES=		gmake fortran
X
XUSE_GITHUB=	yes
XGH_ACCOUNT=	chrchang
XGH_PROJECT=	plink-ng
XGH_TAGNAME=	ebf119
X
XWRKSRC_SUBDIR=	1.9
XMAKEFILE=	Makefile.std
XMAKE_ARGS=	ZLIB=-lz BLASFLAGS="${BLASLIB} ${LAPACKLIB}"
XCFLAGS+=	-DDYNAMIC_ZLIB -I${LOCALBASE}/include
XLDFLAGS+=	-lthr
XINSTALL_TARGET=	install-strip
X
XOPTIONS_DEFINE=		EXAMPLES
XOPTIONS_SINGLE=		BLAS
XOPTIONS_SINGLE_BLAS=	NETLIB OPENBLAS
XOPTIONS_DEFAULT=	OPENBLAS
X
XBLAS_DESC=	BLAS/LAPACK implementation
X
XOPENBLAS_USES=	blaslapack:openblas
X
XNETLIB_DESC=	Netlib's reference
XNETLIB_USES=	blaslapack:netlib
XNETLIB_LIB_DEPENDS=	libcblas.so:math/cblas
XNETLIB_LDFLAGS=	-lcblas
X
XEXAMPLES=	toy.map toy.ped
X
Xpost-build:
X	(cd ${WRKSRC}; ${CC} ${CFLAGS} prettify.c -o prettify)
X
Xpost-install:
X	${INSTALL_PROGRAM} ${WRKSRC}/prettify ${STAGEDIR}${PREFIX}/bin
X
Xpost-install-EXAMPLES-on:
X	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
X	${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/,} ${STAGEDIR}${EXAMPLESDIR}
X
X.include <bsd.port.mk>
3225f885242ffc903c9410142479cfcd
echo x - plink/pkg-plist
sed 's/^X//' >plink/pkg-plist << '03e964e537cb83fc44658a36a53a638a'
Xbin/plink
Xbin/prettify
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/toy.map
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/toy.ped
03e964e537cb83fc44658a36a53a638a
echo x - plink/distinfo
sed 's/^X//' >plink/distinfo << 'a7e532cb61dd2baca4095cee307ed431'
XTIMESTAMP = 1580352274
XSHA256 (chrchang-plink-ng-v1.90b6.15-ebf119_GH0.tar.gz) = 130fc787be200a2b94eccc945e0844e00b9433fc87314c86ef95f3c0160fc012
XSIZE (chrchang-plink-ng-v1.90b6.15-ebf119_GH0.tar.gz) = 2932982
a7e532cb61dd2baca4095cee307ed431
exit