--- Makefile.orig	2015-12-15 21:42:34 UTC
+++ Makefile
@@ -29,16 +29,15 @@ TEST_PROG=  test/test-rbuf
 all: $(PROG) $(TEST_PROG)
 
 # Adjust $(HTSDIR) to point to your top-level htslib directory
-HTSDIR = ../htslib
-include $(HTSDIR)/htslib.mk
-HTSLIB = $(HTSDIR)/libhts.a
-BGZIP  = $(HTSDIR)/bgzip
-TABIX  = $(HTSDIR)/tabix
+HTSDIR = $(prefix)/include
+HTSLIB = -lhts
+BGZIP  = $(HTSDIR)/../bin/bgzip
+TABIX  = $(HTSDIR)/../bin/tabix
 
-CC       = gcc
-CPPFLAGS =
-CFLAGS   = -g -Wall -Wc++-compat -O2
-LDFLAGS  =
+CC       ?= cc
+CPPFLAGS +=
+CFLAGS   += -Wall
+LDFLAGS  +=
 LIBS     =
 
 OBJS     = main.o vcfindex.o tabix.o \
@@ -57,26 +56,20 @@ GSL_LIBS       =
 ifdef USE_GPL
     EXTRA_CPPFLAGS += -DUSE_GPL
     OBJS += polysomy.o peakfit.o
-    GSL_LIBS = -lgsl -lcblas
+    GSL_LIBS = -lgsl -lgslcblas
 endif
 
-prefix      = /usr/local
+prefix      = ${STAGEDIR}${PREFIX}
 exec_prefix = $(prefix)
 bindir      = $(exec_prefix)/bin
 libdir      = $(exec_prefix)/lib
 libexecdir  = $(exec_prefix)/libexec
-mandir      = $(prefix)/share/man
+mandir      = $(prefix)/man
 man1dir     = $(mandir)/man1
 
 plugindir   = $(libexecdir)/bcftools
 pluginpath  = $(plugindir)
 
-MKDIR_P = mkdir -p
-INSTALL = install -p
-INSTALL_PROGRAM = $(INSTALL)
-INSTALL_DATA    = $(INSTALL) -m 644
-INSTALL_DIR     = $(MKDIR_P) -m 755
-
 MISC_PROGRAMS = plot-vcfstats vcfutils.pl plugins/color-chrs.pl
 
 all:$(PROG) plugins
@@ -181,7 +174,7 @@ test/test-rbuf: test/test-rbuf.o
 	$(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS)
 
 bcftools: $(HTSLIB) $(OBJS)
-	$(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)
+	$(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -pthread -lz -lm $(GSL_LIBS) $(LIBS)
 
 doc/bcftools.1: doc/bcftools.txt
 	cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt
@@ -198,8 +191,9 @@ docs: doc/bcftools.1 doc/bcftools.html
 # Since there is no make dependency, bcftools.1 can be out-of-date and
 # make docs can be run to update if asciidoc is available
 install: $(PROG)
-	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
-	$(INSTALL_PROGRAM) $(PROG) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
+	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
+	$(INSTALL_PROGRAM) $(PROG) $(DESTDIR)$(bindir)
+	$(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
 	$(INSTALL_DATA) doc/bcftools.1 $(DESTDIR)$(man1dir)
 	$(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir)