- Update to 0.10

PR:		194309
Submitted by:	jwbacon@tds.net(maintainer)

biology/plinkseq/Makefile

@@ -2,29 +2,39 @@
 # $FreeBSD$
 
 PORTNAME=	plinkseq
-PORTVERSION=	0.08
-PORTREVISION=	3
+PORTVERSION=	0.10
 CATEGORIES=	biology science
-MASTER_SITES=	http://atgu.mgh.harvard.edu/${PORTNAME}/dist/version-${PORTVERSION}/
+MASTER_SITES=	http://psychgen.u.hpc.mssm.edu/plinkseq_downloads/
+# Default DISTNAME is correct, so leave it alone.
+DISTFILES=	${PORTNAME}-src-${PORTVERSION}.tgz
 
 MAINTAINER=	jwbacon@tds.net
 COMMENT=	Toolset for working with human genetic variation data
 
 LICENSE=	GPLv2
 
-LIB_DEPENDS=	libprotobuf.so:${PORTSDIR}/devel/protobuf
-
-USES=		dos2unix libtool shebangfix
-SHEBANG_FILES=	${WRKSRC}/browser/pbrowse.in ${WRKSRC}/index/index.in
-USE_LDCONFIG=	yes
-GNU_CONFIGURE=	yes
-CONFIGURE_ARGS+=--with-protobuf=${LOCALBASE}
+USES=		libtool gmake
 
 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
+	${REINPLACE_CMD} \
+		-e 's|PF_INET|AF_INET|g' \
+		${WRKSRC}/sources/mongoose/sources/lib/mongoose.c
+	${REINPLACE_CMD} \
+		-e 's|g++|${CXX}|g' \
+		-e 's|gcc|${CC}|g' \
+		-e 's|CXXFLAGS = -O3|CXXFLAGS = ${CXXFLAGS}|g' \
+		-e 's|ALL_CFLAGS =-O3|ALL_CFLAGS = ${CFLAGS}|g' \
+		${WRKSRC}/config_defs.Makefile
+	${REINPLACE_CMD} \
+		-e 's| -ldl||g' \
+		-e 's| $$(STATIC_FLAG)||g' \
+		${WRKSRC}/Makefile
+
+do-install:
+.for f in behead browser gcol mm mongoose pdas pseq smp tab2vcf
+	${INSTALL_PROGRAM} ${WRKSRC}/build/execs/${f} ${STAGEDIR}${PREFIX}/bin
+.endfor
+	${INSTALL_DATA} ${WRKSRC}/sources/plinkseq/build/lib/libplinkseq.a \
+		${STAGEDIR}${PREFIX}/lib
 
 .include <bsd.port.mk>

biology/plinkseq/distinfo

@@ -1,2 +1,2 @@
-SHA256 (plinkseq-0.08.tar.gz) = 6bde88925a82a79c6fa2401a197865cf6d659163fd5f11c5fb426701b54bb24f
-SIZE (plinkseq-0.08.tar.gz) = 2991871
+SHA256 (plinkseq-src-0.10.tgz) = e9d4705acf8b22eddba0c48cf502e3bd4236f3b60b010f39f94deecf37e94b58
+SIZE (plinkseq-src-0.10.tgz) = 6090698

biology/plinkseq/files/patch-pp.pb.h

@@ -1,17 +0,0 @@
---- lib/pp.pb.h.orig	2013-03-21 21:46:21.000000000 +0800
-+++ lib/pp.pb.h	2013-03-21 21:46:33.000000000 +0800
-@@ -8,12 +8,12 @@
- 
- #include <google/protobuf/stubs/common.h>
- 
--#if GOOGLE_PROTOBUF_VERSION < 2004000
-+#if GOOGLE_PROTOBUF_VERSION < 2005000
- #error This file was generated by a newer version of protoc which is
- #error incompatible with your Protocol Buffer headers.  Please update
- #error your headers.
- #endif
--#if 2004001 < GOOGLE_PROTOBUF_MIN_PROTOC_VERSION
-+#if 2005001 < GOOGLE_PROTOBUF_MIN_PROTOC_VERSION
- #error This file was generated by an older version of protoc which is
- #error incompatible with your Protocol Buffer headers.  Please
- #error regenerate this file with a newer version of protoc.

biology/plinkseq/files/patch-variant.pb.h

@@ -1,17 +0,0 @@
---- lib/variant.pb.h.orig	2013-03-21 21:45:44.000000000 +0800
-+++ lib/variant.pb.h	2013-03-21 21:45:55.000000000 +0800
-@@ -8,12 +8,12 @@
- 
- #include <google/protobuf/stubs/common.h>
- 
--#if GOOGLE_PROTOBUF_VERSION < 2004000
-+#if GOOGLE_PROTOBUF_VERSION < 2005000
- #error This file was generated by a newer version of protoc which is
- #error incompatible with your Protocol Buffer headers.  Please update
- #error your headers.
- #endif
--#if 2004001 < GOOGLE_PROTOBUF_MIN_PROTOC_VERSION
-+#if 2005001 < GOOGLE_PROTOBUF_MIN_PROTOC_VERSION
- #error This file was generated by an older version of protoc which is
- #error incompatible with your Protocol Buffer headers.  Please
- #error regenerate this file with a newer version of protoc.

biology/plinkseq/pkg-plist

@@ -1,12 +1,10 @@
 bin/behead
+bin/browser
 bin/gcol
-bin/index
-bin/index.cgi
+bin/mm
 bin/mongoose
-bin/pbrowse
-bin/pbrowse.cgi
+bin/pdas
 bin/pseq
+bin/smp
 bin/tab2vcf
-lib/libplinkseq.so
-lib/libplinkseq.so.0
-lib/libplinkseq.so.0.0.0
+lib/libplinkseq.a