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Index: head/biology/bedtools/Makefile
===================================================================
--- head/biology/bedtools/Makefile
+++ head/biology/bedtools/Makefile
@@ -3,6 +3,7 @@
PORTNAME= bedtools
DISTVERSIONPREFIX= v
DISTVERSION= 2.27.1
+PORTREVISION= 1
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
Index: head/biology/bedtools/files/patch-Makefile
===================================================================
--- head/biology/bedtools/files/patch-Makefile
+++ head/biology/bedtools/files/patch-Makefile
@@ -24,6 +24,15 @@
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)
@@ -35,6 +44,18 @@
@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

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