Index: head/biology/migrate/Makefile
===================================================================
--- head/biology/migrate/Makefile	(revision 413498)
+++ head/biology/migrate/Makefile	(revision 413499)
@@ -1,51 +1,52 @@
 # Created by: Johann Visagie <wjv@FreeBSD.org>
 # $FreeBSD$
 
 PORTNAME=	migrate
 PORTVERSION=	3.6.11
 CATEGORIES=	biology
 MASTER_SITES=	http://popgen.sc.fsu.edu/currentversions/
 DISTNAME=	${PORTNAME}-${PORTVERSION}.src
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Program to estimate population sizes and migration rates
 
+WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}/src
+EXTRACT_AFTER_ARGS=--exclude zlib
+
 GNU_CONFIGURE=	yes
 CONFIGURE_ENV=	ac_cv_prog_GMAKE="${MAKE}"
 MAKE_ARGS=	PRETTYCFLAGS="${CFLAGS} -DNOJPEG -DNOZLIB -DNOPNG -Iharu \
 		-DPRETTY -lstdc++"
 
-WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}/src
-
-PLIST_SUB+=	PORTNAME=${PORTNAME}
 PORTDOCS=	HISTORY README README_PARALLEL_GENERAL ${PORTNAME}.html
 PORTEXAMPLES=	*
-EXTRACT_AFTER_ARGS=--exclude zlib
 
-OPTIONS_DEFINE=			DOCS EXAMPLES THREAD
-THREAD_DESC=			Build with THREAD support
-THREAD_ALL_TARGET=		thread
+OPTIONS_DEFINE=		DOCS EXAMPLES THREAD
+THREAD_DESC=		Build with THREAD support
+THREAD_ALL_TARGET=	thread
 
 post-patch:
 	@${REINPLACE_CMD} -e 's|="-O "|="$$CFLAGS"|g' ${WRKSRC}/configure
 	@${REINPLACE_CMD} -e '/PRETTY$$/d' ${WRKSRC}/definitions.h
 	@${REINPLACE_CMD} -e 's|-O3||g' ${WRKSRC}/haru/makefile.gcc
 
 do-install:
 	${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME}-n ${STAGEDIR}${PREFIX}/bin
 	${LN} -sf ${PORTNAME}-n ${STAGEDIR}${PREFIX}/bin/${PORTNAME}
 	${INSTALL_MAN} ${WRKSRC}/${PORTNAME}.1 \
 		${STAGEDIR}${MAN1PREFIX}/man/man1
 	${LN} -sf ${PORTNAME}.1 \
 		${STAGEDIR}${MAN1PREFIX}/man/man1/${PORTNAME}-n.1
 
+do-install-DOCS-on:
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
 	${INSTALL_DATA} ${PORTDOCS:S,^,${WRKSRC}/../,} ${STAGEDIR}${DOCSDIR}
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}/graphics
 	${INSTALL_DATA} ${WRKSRC}/../graphics/* ${STAGEDIR}${DOCSDIR}/graphics
 
+do-install-EXAMPLES-on:
 	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
 	${INSTALL_DATA} ${WRKSRC}/../example/[A-Za-z]* \
 		${STAGEDIR}${EXAMPLESDIR}
 
 .include <bsd.port.mk>
Index: head/biology/migrate/files/patch-Makefile.in
===================================================================
--- head/biology/migrate/files/patch-Makefile.in	(revision 413498)
+++ head/biology/migrate/files/patch-Makefile.in	(revision 413499)
@@ -1,18 +1,18 @@
---- Makefile.in.orig	2013-05-25 14:59:22.000000000 +0000
-+++ Makefile.in	2013-05-25 14:59:37.000000000 +0000
-@@ -89,7 +89,7 @@
+--- Makefile.in.orig	2015-06-24 02:57:05 UTC
++++ Makefile.in
+@@ -89,7 +89,7 @@ PAPERFORMAT       = @PAPERFORMAT@
  # -DINTEGRATEDLIKE may be used to get a marginal likelihood different to the current thermodynamic integr and harmonic mean [does not work]
  # -UEP calculates unique event polymorphism [not checked in a long time -- most likely does not work]
  NEWSTUFF          =  -DNEXUSTREE
 -COMMONFLAGS       = $(ARCH) $(MACOSVERSION) $(NEWSTUFF) $(HAVE_ZNZ) -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS)
 +COMMONFLAGS       = $(MACOSVERSION) $(NEWSTUFF) $(HAVE_ZNZ) -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS)
  #
  # combine the common flags with the version number and subversion number
  COMMONVFLAGS      =  $(COMMONFLAGS)  -DMIGRATESUBVERSION=\"\\\"$(MIGRATESUBVERSION)\\\"\" 
-@@ -544,4 +544,4 @@
+@@ -544,4 +544,4 @@ parallel_short_test::
  #----------------------------------------------------------------
  # BEAGLE
  beagle:
 -	$(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS)  $(BEAGLEFLAGS) $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)"  "LDFLAGS =$(LDFLAGS) $(EXCEPTIONS) `pkg-config /Users/beerli/src/beagle-lib/hmsbeagle-1.0.pc --cflags --libs` -framework OpenCL"
 \ No newline at end of file
 +	$(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS)  $(BEAGLEFLAGS) $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)"  "LDFLAGS =$(LDFLAGS) $(EXCEPTIONS) `pkg-config /Users/beerli/src/beagle-lib/hmsbeagle-1.0.pc --cflags --libs` -framework OpenCL"
Index: head/biology/migrate/pkg-plist
===================================================================
--- head/biology/migrate/pkg-plist	(revision 413498)
+++ head/biology/migrate/pkg-plist	(revision 413499)
@@ -1,8 +1,8 @@
-bin/%%PORTNAME%%
-bin/%%PORTNAME%%-n
-man/man1/%%PORTNAME%%-n.1.gz
-man/man1/%%PORTNAME%%.1.gz
+bin/migrate
+bin/migrate-n
+man/man1/migrate-n.1.gz
+man/man1/migrate.1.gz
 %%PORTDOCS%%%%DOCSDIR%%/graphics/librarian.gif
 %%PORTDOCS%%%%DOCSDIR%%/graphics/mail.gif
-%%PORTDOCS%%%%DOCSDIR%%/graphics/%%PORTNAME%%.gif
+%%PORTDOCS%%%%DOCSDIR%%/graphics/migrate.gif
 %%PORTDOCS%%%%DOCSDIR%%/graphics/packet.gif