Actualiser Makefile

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "sumalibs"]
 	path = sumalibs
-	url = https://git.metabarcoding.org/obitools/sumalibs.git
+	url = https://forge.metabarcoding.org/obitools/sumalibs.git

Makefile

@@ -1,8 +1,12 @@
+PREFIX=/usr/local
+
+CFLAGS=-I$(PREFIX)/include
+
 EXEC = sumatra
 
 SUMATRA_SRC = sumatra.c \
 			  mtcompare_sumatra.c
-			              
+
 SUMATRA_OBJ = $(patsubst %.c,%.o,$(SUMATRA_SRC))
 
 SRCS = $(SUMATRA_SRC)
@@ -22,9 +26,9 @@ all: $(EXEC)
 
 # executable compilation and link
 
-sumatra: $(SUMATRA_OBJ) $(LIBSUMA)
+sumatra: $(SUMATRA_OBJ) ./sumalibs/libsuma.a
 	$(CC) $(LDFLAGS) -o $@ -pthread $(SUMATRA_OBJ) $(LIBSUMAPATH) $(LIB)
-	
+
 ########
 #
 # project management
@@ -32,8 +36,10 @@ sumatra: $(SUMATRA_OBJ) $(LIBSUMA)
 ########
 
 clean:
-	rm -f $(SUMATRA_OBJ)	
+	rm -f $(SUMATRA_OBJ)
 	rm -f $(EXEC)
 	$(MAKE) -C ./sumalibs clean
 
-		
+install: all
+	install -d $(DESTDIR)$(PREFIX)/bin/
+	install -m 755 $(EXEC) $(DESTDIR)$(PREFIX)/bin/

global.mk

@@ -1,4 +1,3 @@
-
 LIBSUMAPATH = -L./sumalibs
 
 LIBSUMA = ./sumalibs/libsuma.a
@@ -8,9 +7,9 @@ LDFLAGS=
 
 
 ifeq ($(CC),gcc)
-        CFLAGS = -O3 -s -DOMP_SUPPORT -w
+        CFLAGS = -I sumalibs -O3 -s -DOMP_SUPPORT -w
 else
-        CFLAGS = -O3 -w
+        CFLAGS = -I sumalibs -O3 -w
 endif
 
 

mtcompare_sumatra.c

@@ -10,10 +10,10 @@
 #include <stdio.h>
 #include <string.h>
 #include "sumatra.h"
-#include "./sumalibs/libfasta/sequence.h"
+#include "libfasta/sequence.h"
-#include "./sumalibs/libutils/utilities.h"
+#include "libutils/utilities.h"
-#include "./sumalibs/liblcs/upperband.h"
+#include "liblcs/upperband.h"
-#include "./sumalibs/liblcs/sse_banded_LCS_alignment.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 "libfasta/sequence.h"
-#include "./sumalibs/liblcs/upperband.h"
+#include "liblcs/upperband.h"
-#include "./sumalibs/liblcs/sse_banded_LCS_alignment.h"
+#include "liblcs/sse_banded_LCS_alignment.h"
-#include "./sumalibs/libutils/utilities.h"
+#include "libutils/utilities.h"
 #include "mtcompare_sumatra.h"
 
-#define VERSION "1.0.32"
+#define VERSION "1.0.36"
 
 
 /* ----------------------------------------------- */

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