svn commit: r370680 - in head/biology/plinkseq: . files

[Wen Heping]

Author: wen
Date: Sun Oct 12 03:16:10 2014
New Revision: 370680
URL: https://svnweb.freebsd.org/changeset/ports/370680
QAT: https://qat.redports.org/buildarchive/r370680/

Log:
  - Update to 0.10
  
  PR:		194309
  Submitted by:	jwbacon at tds.net(maintainer)

Deleted:
  head/biology/plinkseq/files/
Modified:
  head/biology/plinkseq/Makefile
  head/biology/plinkseq/distinfo
  head/biology/plinkseq/pkg-plist

Modified: head/biology/plinkseq/Makefile
==============================================================================
--- head/biology/plinkseq/Makefile	Sun Oct 12 01:51:39 2014	(r370679)
+++ head/biology/plinkseq/Makefile	Sun Oct 12 03:16:10 2014	(r370680)
@@ -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 at 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>

Modified: head/biology/plinkseq/distinfo
==============================================================================
--- head/biology/plinkseq/distinfo	Sun Oct 12 01:51:39 2014	(r370679)
+++ head/biology/plinkseq/distinfo	Sun Oct 12 03:16:10 2014	(r370680)
@@ -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

Modified: head/biology/plinkseq/pkg-plist
==============================================================================
--- head/biology/plinkseq/pkg-plist	Sun Oct 12 01:51:39 2014	(r370679)
+++ head/biology/plinkseq/pkg-plist	Sun Oct 12 03:16:10 2014	(r370680)
@@ -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