$NetBSD$

# Respect the environment
--- Makefile.orig	2016-03-07 07:49:06 UTC
+++ Makefile
@@ -1,5 +1,9 @@
-SAMTOOLS = samtools-1.3
-HTSLIB = htslib-1.3
+# Use ?= to allow overriding standard variables with make arguments or
+# environment variables.  This eliminates the need to edit the Makefile for
+# different platforms and allows package managers to control automated builds.
+
+SAMTOOLS ?= samtools-1.3
+HTSLIB ?= htslib-1.3
 
 ifneq ($(cygwin), true)
   SAMTOOLS_MAKEFILE = Makefile
@@ -7,31 +11,36 @@ else
   SAMTOOLS_MAKEFILE = Makefile.cygwin
 endif
 
-# overridable, defaulting to local copy
-BOOST = .
+# Overridable, defaulting to local copy
+BOOST ?= .
 
 # Compilation variables
-CXX = g++
-CXXFLAGS = -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB)
-CPPFLAGS =
+CXX ?= g++
+# Allow overriding non-portable flags
+CXXFLAGS ?= -Wall
+CXXFLAGS += -std=gnu++98 -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB)
+CPPFLAGS ?=
 
-LDFLAGS =
-LDLIBS =
+LDFLAGS ?=
+LDLIBS ?=
 
 # Installation variables
-INSTALL = install
-INSTALL_PROGRAM = $(INSTALL) -p
-INSTALL_DATA = $(INSTALL) -p -m 644
-INSTALL_DIR = $(INSTALL) -d
-STRIP ?=strip
+INSTALL ?= install
+INSTALL_PROGRAM ?= $(INSTALL) -p
+INSTALL_DATA ?= $(INSTALL) -p -m 644
+INSTALL_DIR ?= $(INSTALL) -d
+STRIP ?= strip
 
-prefix ?= /usr/local
-exec_prefix = $(prefix)
+# PREFIX, not prefix, is used by most package managers
+PREFIX ?= /usr/local
+exec_prefix = $(PREFIX)
 bindir = $(exec_prefix)/bin
+libexecdir ?= $(bindir)
+perl_mod_dir ?= $(bindir)
 
 # Auxiliary variables for compilation
-SAMHEADERS = $(SAMTOOLS)/$(HTSLIB)/htslib/sam.h
-SAMLIBS = $(SAMTOOLS)/$(HTSLIB)/libhts.a
+SAMHEADERS ?= $(SAMTOOLS)/$(HTSLIB)/htslib/sam.h
+SAMLIBS ?= $(SAMTOOLS)/$(HTSLIB)/libhts.a
 CONFIGURE = ./configure
 
 OBJS1 = parseIt.o
@@ -158,12 +167,15 @@ ebseq :
 
 # Install RSEM
 install : $(PROGRAMS) $(SCRIPTS) $(SAMTOOLS)/samtools rsem_perl_utils.pm
-	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/$(SAMTOOLS)
+	$(INSTALL_DIR) \
+		$(DESTDIR)$(bindir) \
+		$(DESTDIR)$(libexecdir)/rsem \
+		$(DESTDIR)$(perl_mod_dir)
 	$(foreach prog,$(PROGRAMS),$(INSTALL_PROGRAM) $(prog) $(DESTDIR)$(bindir)/$(prog) ; $(STRIP) $(DESTDIR)$(bindir)/$(prog) ;)
-	$(INSTALL_PROGRAM) $(SAMTOOLS)/samtools $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools
-	$(STRIP) $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools
-	$(foreach script,$(SCRIPTS),$(INSTALL_PROGRAM) $(script) $(DESTDIR)$(bindir)/$(script) ;)
-	$(INSTALL_DATA) rsem_perl_utils.pm $(DESTDIR)$(bindir)/rsem_perl_utils.pm
+	$(INSTALL_PROGRAM) $(SAMTOOLS)/samtools $(DESTDIR)$(libexecdir)/rsem
+	$(STRIP) $(DESTDIR)$(libexecdir)/rsem/samtools
+	$(foreach script,$(SCRIPTS),$(INSTALL_PROGRAM) $(script) $(DESTDIR)$(bindir) ;)
+	$(INSTALL_DATA) rsem_perl_utils.pm $(DESTDIR)$(perl_mod_dir)
 
 # Clean
 clean :