Index: head/biology/mummer/Makefile
===================================================================
--- head/biology/mummer/Makefile	(revision 453151)
+++ head/biology/mummer/Makefile	(revision 453152)
@@ -1,31 +1,47 @@
 # Created by: Tony Maher
 # $FreeBSD$
 
 PORTNAME=	mummer
 PORTVERSION=	3.23
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	biology
 MASTER_SITES=	SF
 DISTNAME=	MUMmer${PORTVERSION}
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Modular system for rapid whole genome alignment
 
-USES=		gmake perl5
+LICENSE=	ART10
+LICENSE_FILE=	${WRKSRC}/LICENSE
 
+USES=		gmake perl5 shebangfix
+
+SHEBANG_FILES=	scripts/*.csh scripts/*.pl
+SHEBANG_LANG=	csh
+perl_OLD_CMD=	__PERL_PATH
+csh_OLD_CMD=	__CSH_PATH
+csh_CMD=	/bin/csh
+_SHEBANG_REINPLACE_ARGS+=	-e "s|__BIN_DIR|${PREFIX}/bin|g;s|__AUX_BIN_DIR|${PREFIX}/libexec/mummer|g;s|__SCRIPT_DIR|${PREFIX}/libexec/mummer|g"
+
 PROGRAMS=	annotate combineMUMs delta-filter gaps \
 		mgaps mummer repeat-match show-aligns \
 		show-coords show-diff show-snps show-tiling
-SCRIPTS=	dnadiff exact-tandems mapview mummerplot nucmer \
-		nucmer2xfig promer run-mummer1 run-mummer3
+SCRIPTS=	dnadiff.pl exact-tandems.csh mapview.pl mummerplot.pl nucmer.pl \
+		nucmer2xfig.pl promer.pl run-mummer1.csh run-mummer3.csh
+LIBEXEC=	Foundation.pm tandem-repeat.awk
 DOCUMENTS=	COPYRIGHT INSTALL LICENSE README
 
 OPTIONS_DEFINE=	DOCS
 
 do-install:
 	${INSTALL_PROGRAM} ${PROGRAMS:S|^|${WRKSRC}/|} ${STAGEDIR}${PREFIX}/bin
-	${INSTALL_SCRIPT} ${SCRIPTS:S|^|${WRKSRC}/|} ${STAGEDIR}${PREFIX}/bin
+.for file in ${SCRIPTS}
+	${INSTALL_SCRIPT} ${WRKSRC}/scripts/${file} ${STAGEDIR}${PREFIX}/bin/${file:R}
+.endfor
+	@${MKDIR} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME}
+	${INSTALL_PROGRAM} ${WRKSRC}/aux_bin/* ${STAGEDIR}${PREFIX}/libexec/${PORTNAME}
+	${INSTALL_DATA} ${LIBEXEC:S|^|${WRKSRC}/scripts/|} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME}
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
 	${INSTALL_DATA} ${DOCUMENTS:S|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR}
 
 .include <bsd.port.mk>
Index: head/biology/mummer/distinfo
===================================================================
--- head/biology/mummer/distinfo	(revision 453151)
+++ head/biology/mummer/distinfo	(revision 453152)
@@ -1,2 +1,3 @@
+TIMESTAMP = 1509357521
 SHA256 (MUMmer3.23.tar.gz) = 1efad4f7d8cee0d8eaebb320a2d63745bb3a160bb513a15ef7af46f330af662f
 SIZE (MUMmer3.23.tar.gz) = 3160143
Index: head/biology/mummer/files/patch-Makefile
===================================================================
--- head/biology/mummer/files/patch-Makefile	(revision 453151)
+++ head/biology/mummer/files/patch-Makefile	(revision 453152)
@@ -1,20 +1,28 @@
---- Makefile.orig	2015-08-05 01:03:53 UTC
+--- Makefile.orig	2011-12-17 02:49:27 UTC
 +++ Makefile
 @@ -35,16 +35,11 @@ SCRIPT_DIR    := $(TOP_DIR)/scripts
  TIGR_SRC_DIR  := $(TOP_DIR)/src/tigr
  KURTZ_SRC_DIR := $(TOP_DIR)/src/kurtz
  
 -CC   := $(filter /%,$(shell /bin/sh -c 'type gcc'))
 -CXX  := $(filter /%,$(shell /bin/sh -c 'type g++'))
  SED  := $(filter /%,$(shell /bin/sh -c 'type sed'))
  CSH  := $(filter /%,$(shell /bin/sh -c 'type csh'))
--PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
-+PERL := ${LOCALBASE}/bin/perl
+ PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
  AR   := $(filter /%,$(shell /bin/sh -c 'type ar'))
  
 -CXXFLAGS = -O3
 -CFLAGS = -O3
 -LDFLAGS  =
  
  FLATS = ACKNOWLEDGEMENTS COPYRIGHT INSTALL LICENSE Makefile README ChangeLog
  
+@@ -60,7 +55,7 @@ export BIN_DIR AUX_BIN_DIR CXX CC CFLAGS
+ .PHONY: all check clean dist scripts uninstall
+ 
+ 
+-all: kurtz tigr scripts
++all: kurtz tigr
+ 
+ 
+ check:
Index: head/biology/mummer/pkg-plist
===================================================================
--- head/biology/mummer/pkg-plist	(revision 453151)
+++ head/biology/mummer/pkg-plist	(revision 453152)
@@ -1,25 +1,31 @@
 bin/annotate
 bin/combineMUMs
 bin/delta-filter
 bin/dnadiff
 bin/exact-tandems
 bin/gaps
 bin/mapview
 bin/mgaps
 bin/mummer
 bin/mummerplot
 bin/nucmer
 bin/nucmer2xfig
 bin/promer
 bin/repeat-match
 bin/run-mummer1
 bin/run-mummer3
 bin/show-aligns
 bin/show-coords
 bin/show-diff
 bin/show-snps
 bin/show-tiling
+libexec/mummer/Foundation.pm
+libexec/mummer/postnuc
+libexec/mummer/postpro
+libexec/mummer/prenuc
+libexec/mummer/prepro
+libexec/mummer/tandem-repeat.awk
 %%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
 %%PORTDOCS%%%%DOCSDIR%%/INSTALL
 %%PORTDOCS%%%%DOCSDIR%%/LICENSE
 %%PORTDOCS%%%%DOCSDIR%%/README