From 6fe3ffa44a450bd83f6df6b6ca4a200b97a47936 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Fri, 12 Jun 2009 13:50:53 +0000
Subject: [PATCH]  * update Makefile  * update INSTALL instruction

---
 INSTALL       | 32 ++++++++++++++++++++++++--------
 Makefile      | 14 ++++++++------
 misc/Makefile |  2 +-
 zlib/Makefile |  2 +-
 4 files changed, 34 insertions(+), 16 deletions(-)

diff --git a/INSTALL b/INSTALL
index faa3eaf..f202463 100644
--- a/INSTALL
+++ b/INSTALL
@@ -1,8 +1,24 @@
-Compiling samtools requires the zlib library <http://www.zlib.net/>;
-compiling the alignment viewer further requires the GNU ncurses library
-<http://www.gnu.org/software/ncurses/>.
-
-Please type `./configure; make' to compile samtools. If it fails, try
-`make -f Makefile.generic'. If the compilation still fails due to errors
-in RAZF or the lack of ncurses, try `make -f Makefile.lite' to disable
-the alignment viewer and the RAZF-enhanced FASTA indexer.
+System Requirements
+===================
+
+Most of SAMtools functionality only depends on zlib which is included in
+this source code package. Compiling the alignment viewer further
+requires the GNU ncurses library <http://www.gnu.org/software/ncurses/>,
+which comes with Mac OS X and most of the modern Linux/Unix
+distributions. If you do not have this library installed, you can still
+compile the rest of SAMtools by manually modifying two lines in Makefile
+as is described in the Makefile.
+
+
+Compilation
+===========
+
+Type `make' to compile samtools.
+
+
+Installation
+============
+
+Simply copy `samtools' and other executables/scripts in `misc' to a
+location you want (e.g. a directory in your $PATH). No further
+configurations are required.
diff --git a/Makefile b/Makefile
index 6bf4227..86612c1 100644
--- a/Makefile
+++ b/Makefile
@@ -1,16 +1,17 @@
 CC=			gcc
 CXX=		g++
-CFLAGS=		-g -Wall #-O2 -m64 #-arch ppc
+CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
 CXXFLAGS=	$(CFLAGS)
-DFLAGS=		-D_IOLIB=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 #-D_NO_RAZF #-D_NO_CURSES
+### For ncurses: please apply `-D_NO_CURSES' if you do not have ncurses installed
+DFLAGS=		-D_IOLIB=2 -D_FILE_OFFSET_BITS=64 #-D_NO_CURSES
 OBJS=		bam.o bam_import.o bam_pileup.o bam_lpileup.o bam_sort.o bam_index.o \
 			razf.o bgzf.o faidx.o bam_tview.o bam_maqcns.o bam_aux.o bam_plcmd.o \
 			bam_mate.o bam_rmdup.o glf.o bam_stat.o kstring.o bam_md.o sam.o sam_view.o \
 			bam_rmdupse.o
 PROG=		razip bgzip samtools
-INCLUDES=	
-LIBS=		-lm -lz
-SUBDIRS=	. misc
+INCLUDES=	-Izlib
+LIBS=		-lm -Lzlib -lz
+SUBDIRS=	zlib . misc
 
 .SUFFIXES:.c .o
 
@@ -22,7 +23,7 @@ all-recur lib-recur clean-recur cleanlocal-recur install-recur:
 		wdir=`pwd`; \
 		list='$(SUBDIRS)'; for subdir in $$list; do \
 			cd $$subdir; \
-			$(MAKE) -f Makefile.generic CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
+			$(MAKE) -f Makefile CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
 				INCLUDES="$(INCLUDES)" LIBS="$(LIBS)" $$target || exit 1; \
 			cd $$wdir; \
 		done;
@@ -34,6 +35,7 @@ lib:libbam.a
 libbam.a:$(OBJS)
 		$(AR) -cru $@ $(OBJS)
 
+### For ncurses: comment out `-lcurses' if you do not have ncurses installed
 samtools:lib bamtk.o
 		$(CC) $(CFLAGS) -o $@ bamtk.o $(LIBS) -L. -lbam -lcurses
 
diff --git a/misc/Makefile b/misc/Makefile
index 6d69292..4b1bae5 100644
--- a/misc/Makefile
+++ b/misc/Makefile
@@ -2,7 +2,7 @@ CC=			gcc
 CXX=		g++
 CFLAGS=		-g -Wall -O2 -m64 #-arch ppc
 CXXFLAGS=	$(CFLAGS)
-DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
+DFLAGS=		-D_FILE_OFFSET_BITS=64
 OBJS=		
 PROG=		faidx md5sum-lite md5fa maq2sam-short maq2sam-long wgsim
 INCLUDES=	-I..
diff --git a/zlib/Makefile b/zlib/Makefile
index ea4c7f1..9f4210d 100644
--- a/zlib/Makefile
+++ b/zlib/Makefile
@@ -31,7 +31,7 @@ uncompr.o: zlib.h zconf.h
 zutil.o: zutil.h zlib.h zconf.h
 
 cleanlocal:
-		rm -f *.o a.out *~ *.a libzr.a gmon.out
+		rm -f *.o a.out *~ *.a libz.a gmon.out
 
 clean:cleanlocal
 
-- 
2.39.2