--- Makefile.orig	2015-12-15 21:26:20 UTC
+++ Makefile
@@ -39,18 +39,18 @@ AOBJS=      bam_index.o bam_plcmd.o sam_
             bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \
             bam_quickcheck.o bam_addrprg.o
 
-prefix      = /usr/local
+prefix      = ${STAGEDIR}${PREFIX}
 exec_prefix = $(prefix)
 bindir      = $(exec_prefix)/bin
 datarootdir = $(prefix)/share
-mandir      = $(datarootdir)/man
+mandir      = $(prefix)/man
 man1dir     = $(mandir)/man1
 
-MKDIR_P = mkdir -p
-INSTALL = install -p
-INSTALL_PROGRAM = $(INSTALL)
-INSTALL_DATA    = $(INSTALL) -m 644
-INSTALL_DIR     = $(MKDIR_P) -m 755
+#MKDIR_P = mkdir -p
+#INSTALL = install -p
+#INSTALL_PROGRAM = $(INSTALL)
+#INSTALL_DATA    = $(INSTALL) -m 644
+#INSTALL_DIR     = $(MKDIR_P) -m 755
 
 
 PROGRAMS = samtools
@@ -60,7 +60,6 @@ BUILT_MISC_PROGRAMS = \
 	misc/md5fa misc/md5sum-lite misc/wgsim
 
 MISC_PROGRAMS = \
-	$(BUILT_MISC_PROGRAMS) \
 	misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \
 	misc/interpolate_sam.pl misc/novo2sam.pl \
 	misc/plot-bamstats misc/psl2sam.pl \
@@ -81,9 +80,9 @@ BUILT_TEST_PROGRAMS = \
 all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS)
 
 # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally
-ALL_CPPFLAGS = $(DFLAGS) -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
+ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
 ALL_LDFLAGS  = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS)
-ALL_LIBS     = -lz -ldl $(LIBS)
+ALL_LIBS     = -lz $(LIBS)
 
 # Usually config.mk and config.h are generated by running configure
 # or config.status, but if those aren't used create defaults here.
@@ -280,8 +279,10 @@ misc/maq2sam-long.o: misc/maq2sam.c
 
 
 install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
-	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir)
-	$(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
+	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir) 
+	$(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
+	$(INSTALL_PROGRAM) $(BUILT_MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
+	$(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
 	$(INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir)