6 files changed, 94 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 6044da1ad279..e113e4078e36 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -114,6 +114,7 @@
     SUBDIR += phred
     SUBDIR += phylip
     SUBDIR += phyml
+    SUBDIR += plink
     SUBDIR += plinkseq
     SUBDIR += primer3
     SUBDIR += prodigal
diff --git a/biology/plink/Makefile b/biology/plink/Makefile
new file mode 100644
index 000000000000..e8c5ee1d5c5b
--- /dev/null
+++ b/biology/plink/Makefile
@@ -0,0 +1,57 @@
+# $FreeBSD$
+
+PORTNAME=		plink
+DISTVERSIONPREFIX=	v
+DISTVERSION=		1.90b6.17
+CATEGORIES=		biology
+
+MAINTAINER=	mzaki@e-mail.ne.jp
+COMMENT=	Whole genome association analysis toolset
+
+LICENSE=	GPLv3
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+NOT_FOR_ARCHS=		aarch64 mips64 powerpc64 sparc64
+NOT_FOR_ARCHS_REASON=	64bit code requires SSE2 instructions
+
+USES=		gmake fortran
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	chrchang
+GH_PROJECT=	plink-ng
+GH_TAGNAME=	79b2df8c
+
+WRKSRC_SUBDIR=	1.9
+MAKEFILE=	Makefile.std
+MAKE_ARGS=	ZLIB=-lz BLASFLAGS="${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>
diff --git a/biology/plink/distinfo b/biology/plink/distinfo
new file mode 100644
index 000000000000..619b5b786086
--- /dev/null
+++ b/biology/plink/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1588630386
+SHA256 (chrchang-plink-ng-v1.90b6.17-79b2df8c_GH0.tar.gz) = 1207dcabb4bf3f3f4ec5b0e4e5d66ec14075e2cd6d45dd318f13dfb8b4e57116
+SIZE (chrchang-plink-ng-v1.90b6.17-79b2df8c_GH0.tar.gz) = 3013121
diff --git a/biology/plink/files/patch-plink__common.h b/biology/plink/files/patch-plink__common.h
new file mode 100644
index 000000000000..60701bb60b4e
--- /dev/null
+++ b/biology/plink/files/patch-plink__common.h
@@ -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
diff --git a/biology/plink/pkg-descr b/biology/plink/pkg-descr
new file mode 100644
index 000000000000..ba35b2b902ee
--- /dev/null
+++ b/biology/plink/pkg-descr
@@ -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/
diff --git a/biology/plink/pkg-plist b/biology/plink/pkg-plist
new file mode 100644
index 000000000000..c646d6a309ff
--- /dev/null
+++ b/biology/plink/pkg-plist
@@ -0,0 +1,4 @@
+bin/plink
+bin/prettify
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/toy.map
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/toy.ped