Index: biology/plink/Makefile
===================================================================
--- biology/plink/Makefile	(nonexistent)
+++ biology/plink/Makefile	(working copy)
@@ -0,0 +1,57 @@
+# $FreeBSD$
+
+PORTNAME=	plink
+DISTVERSIONPREFIX=	v
+DISTVERSION=	1.90b6.16
+CATEGORIES=	biology
+
+MAINTAINER=	mzaki@e-mail.ne.jp
+COMMENT=	Whole genome association analysis toolset
+
+LICENSE=	GPLv3
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+NOT_FOR_ARCHS=	aarch64 mips64 powerpc64 sparc64
+NOT_FOR_ARCHS_REASON=	64bit code requires SSE2 instructions
+
+USES=		gmake fortran
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	chrchang
+GH_PROJECT=	plink-ng
+GH_TAGNAME=	a2002c8
+
+WRKSRC_SUBDIR=	1.9
+MAKEFILE=	Makefile.std
+MAKE_ARGS=	ZLIB=-lz BLASFLAGS="${BLASLIB} ${LAPACKLIB}"
+CFLAGS+=	-DDYNAMIC_ZLIB -I${LOCALBASE}/include
+LDFLAGS+=	-lthr
+INSTALL_TARGET=	install-strip
+
+OPTIONS_DEFINE=		EXAMPLES
+OPTIONS_SINGLE=		BLAS
+OPTIONS_SINGLE_BLAS=	NETLIB OPENBLAS
+OPTIONS_DEFAULT=	OPENBLAS
+
+BLAS_DESC=	BLAS/LAPACK implementation
+
+OPENBLAS_USES=	blaslapack:openblas
+
+NETLIB_DESC=	Netlib's reference
+NETLIB_USES=	blaslapack:netlib
+NETLIB_LIB_DEPENDS=	libcblas.so:math/cblas
+NETLIB_LDFLAGS=	-lcblas
+
+EXAMPLES=	toy.map toy.ped
+
+post-build:
+	(cd ${WRKSRC}; ${CC} ${CFLAGS} prettify.c -o prettify)
+
+post-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/prettify ${STAGEDIR}${PREFIX}/bin
+
+post-install-EXAMPLES-on:
+	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
+	${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/,} ${STAGEDIR}${EXAMPLESDIR}
+
+.include <bsd.port.mk>

Property changes on: biology/plink/Makefile
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:keywords
## -0,0 +1 ##
+FreeBSD=%H
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## -0,0 +1 ##
+text/plain
\ No newline at end of property
Index: biology/plink/distinfo
===================================================================
--- biology/plink/distinfo	(nonexistent)
+++ biology/plink/distinfo	(working copy)
@@ -0,0 +1,3 @@
+TIMESTAMP = 1582006725
+SHA256 (chrchang-plink-ng-v1.90b6.16-a2002c8_GH0.tar.gz) = 34524ae326d4f547cc49961a2ca66ca2d80d1c34eb8d9d977ec9a78005d20643
+SIZE (chrchang-plink-ng-v1.90b6.16-a2002c8_GH0.tar.gz) = 2985789

Property changes on: biology/plink/distinfo
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Index: biology/plink/files/patch-plink__common.h
===================================================================
--- biology/plink/files/patch-plink__common.h	(nonexistent)
+++ biology/plink/files/patch-plink__common.h	(working copy)
@@ -0,0 +1,20 @@
+--- plink_common.h.orig	2020-01-22 01:51:56 UTC
++++ plink_common.h
+@@ -122,7 +122,7 @@
+   #define EOLN_STR "\n"
+   #define FOPEN_RB "r"
+   #define FOPEN_WB "w"
+-  #ifndef __APPLE__
++  #if !defined(__APPLE__) && !defined(__FreeBSD__)
+     // argh
+     // not sure what the right threshold actually is, but this works for now
+     // (may break on gcc <3.0?  but that shouldn't matter anymore)
+@@ -143,7 +143,7 @@
+   #define CLZLU __builtin_clzl
+   #ifndef __LP64__
+     // attempt to patch GCC 6 build failure
+-    #if (__GNUC__ <= 4) && (__GNUC_MINOR__ < 8)
++    #if !defined(__FreeBSD__) && (__GNUC__ <= 4) && (__GNUC_MINOR__ < 8)
+       #ifndef uintptr_t
+         #define uintptr_t unsigned long
+       #endif

Property changes on: biology/plink/files/patch-plink__common.h
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Added: fbsd:nokeywords
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+yes
\ No newline at end of property
Added: svn:eol-style
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+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Index: biology/plink/pkg-descr
===================================================================
--- biology/plink/pkg-descr	(nonexistent)
+++ biology/plink/pkg-descr	(working copy)
@@ -0,0 +1,9 @@
+PLINK is a widely used toolset for genome-wide association studies (GWAS) and
+research in population genetics.
+
+Citation:
+Chang et al. (2015)
+Second-generation PLINK: rising to the challenge of larger and richer datasets.
+GigaScience 4(1) doi:10.1186/s13742-015-0047-8
+
+WWW: https://www.cog-genomics.org/plink/

Property changes on: biology/plink/pkg-descr
___________________________________________________________________
Added: fbsd:nokeywords
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+yes
\ No newline at end of property
Added: svn:eol-style
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+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Index: biology/plink/pkg-plist
===================================================================
--- biology/plink/pkg-plist	(nonexistent)
+++ biology/plink/pkg-plist	(working copy)
@@ -0,0 +1,4 @@
+bin/plink
+bin/prettify
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/toy.map
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/toy.ped

Property changes on: biology/plink/pkg-plist
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
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+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property