Index: head/biology/bedtools/Makefile
===================================================================
--- head/biology/bedtools/Makefile	(revision 472559)
+++ head/biology/bedtools/Makefile	(revision 472560)
@@ -1,30 +1,31 @@
 # $FreeBSD$
 
 PORTNAME=	bedtools
 DISTVERSIONPREFIX=	v
 DISTVERSION=	2.27.1
+PORTREVISION=	1
 CATEGORIES=	biology
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Toolset for genome set arithmetic such as intersect, union
 
 LICENSE=	GPLv2
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 USES=		gmake python
 USE_GITHUB=	yes
 GH_ACCOUNT=	arq5x
 GH_PROJECT=	bedtools2
 
 pre-build:
 	@${REINPLACE_CMD} -e 's|python|${PYTHON_CMD}|g' ${WRKSRC}/Makefile
 	@${REINPLACE_CMD} -e 's|@\$$(CXX)|$$(CXX)|g' \
 		${WRKSRC}/*/Makefile \
 		${WRKSRC}/*/*/Makefile \
 		${WRKSRC}/*/*/*/Makefile \
 		${WRKSRC}/*/*/*/*/Makefile
 
 post-install:
 	${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/bedtools
 
 .include <bsd.port.mk>
Index: head/biology/bedtools/files/patch-Makefile
===================================================================
--- head/biology/bedtools/files/patch-Makefile	(revision 472559)
+++ head/biology/bedtools/files/patch-Makefile	(revision 472560)
@@ -1,46 +1,67 @@
 --- Makefile.orig	2017-12-14 17:15:02 UTC
 +++ Makefile
 @@ -4,7 +4,7 @@
  # (c) 2009 Aaron Quinlan
  # ==========================
  
 -SHELL := /bin/bash -e
 +SHELL := /bin/sh -e
  
  VERSION_FILE=./src/utils/version/version_git.h
  RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
 @@ -16,11 +16,11 @@ export OBJ_DIR	= obj
  export BIN_DIR	= bin
  export SRC_DIR	= src
  export UTIL_DIR	= src/utils
 -export CXX		= g++
 +export CXX		?= g++
  ifeq ($(DEBUG),1)
 -export CXXFLAGS = -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
 +export CXXFLAGS += -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
  else
 -export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
 +export CXXFLAGS += -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
  endif
  
  # If the user has specified to do so, tell the compile to use rand() (instead of mt19937).
+@@ -33,7 +33,7 @@ endif 
+ export LIBS		= -lz
+ export BT_ROOT  = src/utils/BamTools/
+ 
+-prefix ?= /usr/local
++PREFIX ?= /usr/local
+ 
+ SUBDIRS = $(SRC_DIR)/annotateBed \
+ 		  $(SRC_DIR)/bamToBed \
 @@ -143,8 +143,8 @@ INCLUDES =	-I$(SRC_DIR)/utils/bedFile \
  
  all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)
  	@echo "- Building main bedtools binary."
 -	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
 -	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
 +	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
 +	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
  	@echo "done."
  
  	@echo "- Creating executables for old CLI."
+@@ -156,9 +156,9 @@ all: print_banner $(OBJ_DIR) $(BIN_DIR) 
+ .PHONY: all
+ 
+ install: all
+-	mkdir -p $(DESTDIR)$(prefix)/bin
++	mkdir -p $(DESTDIR)$(PREFIX)/bin
+ 	for file in bin/* ; do \
+-		cp -f $$file $(DESTDIR)$(prefix)/bin; \
++		cp -f $$file $(DESTDIR)$(PREFIX)/bin; \
+ 	done
+ 
+ print_banner:
 @@ -193,7 +193,7 @@ clean:
  .PHONY: clean
  
  test: all
 -	@cd test; bash test.sh
 +	@cd test; $(SHELL) test.sh
  
  .PHONY: test