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>

9 files changed, 138 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 3134c5ddf4d0..4956b22f782c 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -72,6 +72,8 @@
     SUBDIR += phylip
     SUBDIR += phyml
     SUBDIR += platon
+    SUBDIR += plink
+    SUBDIR += plinkseq
     SUBDIR += povchem
     SUBDIR += primer3
     SUBDIR += protomol
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/
diff --git a/biology/plinkseq/Makefile b/biology/plinkseq/Makefile
new file mode 100644
index 000000000000..7870f3024291
--- /dev/null
+++ b/biology/plinkseq/Makefile
@@ -0,0 +1,28 @@
+# Created by: Jason Bacon <jwbacon@tds.net>
+# $FreeBSD$
+
+PORTNAME=	plinkseq
+PORTVERSION=	0.08
+CATEGORIES=	biology science
+MASTER_SITES=	http://atgu.mgh.harvard.edu/${PORTNAME}/dist/version-${PORTVERSION}/
+
+MAINTAINER=	jwbacon@tds.net
+COMMENT=	Toolset for working with human genetic variation data
+
+LICENSE=	GPLv2
+
+LIB_DEPENDS=	protobuf:${PORTSDIR}/devel/protobuf
+
+USE_DOS2UNIX=	yes
+USE_LDCONFIG=	yes
+GNU_CONFIGURE=	yes
+CONFIGURE_ARGS+=--with-protobuf=${LOCALBASE}
+
+post-patch:
+	${REINPLACE_CMD} -e 's|PF_INET|AF_INET|g' ${WRKSRC}/browser/mongoose.c
+	${REINPLACE_CMD} -e 's|-ldl||g' \
+		${WRKSRC}/browser/Makefile.in \
+		${WRKSRC}/client/Makefile.in \
+		${WRKSRC}/index/Makefile.in
+
+.include <bsd.port.mk>
diff --git a/biology/plinkseq/distinfo b/biology/plinkseq/distinfo
new file mode 100644
index 000000000000..daeff2173c24
--- /dev/null
+++ b/biology/plinkseq/distinfo
@@ -0,0 +1,2 @@
+SHA256 (plinkseq-0.08.tar.gz) = 6bde88925a82a79c6fa2401a197865cf6d659163fd5f11c5fb426701b54bb24f
+SIZE (plinkseq-0.08.tar.gz) = 2991871
diff --git a/biology/plinkseq/pkg-descr b/biology/plinkseq/pkg-descr
new file mode 100644
index 000000000000..1d7356738a2a
--- /dev/null
+++ b/biology/plinkseq/pkg-descr
@@ -0,0 +1,8 @@
+PLINK/SEQ is an open-source C/C++ library for working with human
+genetic variation data. The specific focus is to provide a platform
+for analytic tool development for variation data from large-scale
+resequencing and genotyping projects, particularly whole-exome and
+whole-genome studies. It is independent of (but designed to be
+complementary to) the existing PLINK package.
+
+WWW: http://atgu.mgh.harvard.edu/plinkseq/
diff --git a/biology/plinkseq/pkg-plist b/biology/plinkseq/pkg-plist
new file mode 100644
index 000000000000..a277471b3498
--- /dev/null
+++ b/biology/plinkseq/pkg-plist
@@ -0,0 +1,12 @@
+bin/behead
+bin/gcol
+bin/index
+bin/index.cgi
+bin/mongoose
+bin/pbrowse
+bin/pbrowse.cgi
+bin/pseq
+bin/tab2vcf
+lib/libplinkseq.la
+lib/libplinkseq.so
+lib/libplinkseq.so.0