forgotten pdf doc

Makefile

@@ -1,3 +1,7 @@
+PREFIX=/usr/local
+
+CFLAGS=-I$(PREFIX)/include
+
 EXEC = sumatra
 
 SUMATRA_SRC = sumatra.c \
@@ -22,7 +26,7 @@ all: $(EXEC)
 
 # executable compilation and link
 
-sumatra: $(SUMATRA_OBJ) $(LIBSUMA)
+sumatra: $(SUMATRA_OBJ)
 	$(CC) $(LDFLAGS) -o $@ -pthread $(SUMATRA_OBJ) $(LIBSUMAPATH) $(LIB)
 	
 ########
@@ -36,4 +40,6 @@ clean:
 	rm -f $(EXEC)
 	$(MAKE) -C ./sumalibs clean
 
-		
+install: all
+	install -d $(DESTDIR)$(PREFIX)/bin/
+	install -m 755 $(EXEC) $(DESTDIR)$(PREFIX)/bin/

mtcompare_sumatra.c

@@ -10,10 +10,10 @@
 #include <stdio.h>
 #include <string.h>
 #include "sumatra.h"
-#include "./sumalibs/libfasta/sequence.h"
-#include "./sumalibs/libutils/utilities.h"
-#include "./sumalibs/liblcs/upperband.h"
-#include "./sumalibs/liblcs/sse_banded_LCS_alignment.h"
+#include "libfasta/sequence.h"
+#include "libutils/utilities.h"
+#include "liblcs/upperband.h"
+#include "liblcs/sse_banded_LCS_alignment.h"
 
 
 typedef struct {

sumatra.c

@@ -14,13 +14,13 @@
 
 #include <sys/time.h>
 
-#include "./sumalibs/libfasta/sequence.h"
-#include "./sumalibs/liblcs/upperband.h"
-#include "./sumalibs/liblcs/sse_banded_LCS_alignment.h"
-#include "./sumalibs/libutils/utilities.h"
+#include "libfasta/sequence.h"
+#include "liblcs/upperband.h"
+#include "liblcs/sse_banded_LCS_alignment.h"
+#include "libutils/utilities.h"
 #include "mtcompare_sumatra.h"
 
-#define VERSION "1.0.32"
+#define VERSION "1.0.34"
 
 
 /* ----------------------------------------------- */

sumatra.h

@@ -8,7 +8,7 @@
 #ifndef SUMATRA_H_
 #define SUMATRA_H_
 
-#include "./sumalibs/libfasta/sequence.h"
+#include "libfasta/sequence.h"
 
 void printResults(fastaSeqPtr seq1, fastaSeqPtr seq2, double score, BOOL extradata, int64_t pairs, BOOL print);
 

sumatra_user_manual.md

@@ -29,7 +29,8 @@ Untar the archive, go into the newly created directory and compile:
 ```
 tar –zxvf sumatra_v[x.x.xx].tar.gz
 cd sumatra_v[x.x.xx]
-make
+make -C sumalibs install
+make install
 ```
 
 ## Documentation