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--- Makefile.orig 2021-01-23 19:33:26 UTC
+++ Makefile
@@ -4,7 +4,8 @@
# (c) 2009 Aaron Quinlan
# ==========================
-SHELL := /bin/bash -e
+# Use sh for portability and avoid bash extensions in shell commands
+SHELL := /bin/sh -e
VERSION_FILE=./src/utils/version/version_git.h
RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
@@ -21,7 +22,8 @@ OBJ_DIR = obj
BIN_DIR = bin
SRC_DIR = src
-CXX = g++
+# Default if not provided via the environment or make args
+CXX ?= g++
ifeq ($(DEBUG),1)
BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
@@ -41,7 +43,8 @@ endif
BT_LDFLAGS =
BT_LIBS = -lz -lm -lbz2 -llzma -lpthread
-prefix ?= /usr/local
+# Default if not provided via the environment or make args
+PREFIX ?= /usr/local
SUBDIRS = $(SRC_DIR)/annotateBed \
$(SRC_DIR)/bamToBed \
@@ -197,9 +200,9 @@ $(BIN_DIR)/intersectBed: | $(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
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