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

@@ -1,14 +1,17 @@
-EXEC=sumatra
+PREFIX=/usr/local
 
-SUMATRA_SRC= sumatra.c \
+CFLAGS=-I$(PREFIX)/include
-			 mtcompare_sumatra.c
-			              
-SUMATRA_OBJ= $(patsubst %.c,%.o,$(SUMATRA_SRC))
 
+EXEC = sumatra
 
-SRCS= $(SUMATRA_SRC)
+SUMATRA_SRC = sumatra.c \
+			  mtcompare_sumatra.c
 
-LIB= -lfasta -llcs -lfile -lutils -lz -lm
+SUMATRA_OBJ = $(patsubst %.c,%.o,$(SUMATRA_SRC))
+
+SRCS = $(SUMATRA_SRC)
+
+LIB = -lsuma -lz -lm
 
 include ./global.mk
 
@@ -23,9 +26,9 @@ all: $(EXEC)
 
 # executable compilation and link
 
-sumatra: $(SUMATRA_OBJ) $(LIBFASTA) $(LIBLCS) $(LIBFILE) $(LIBUTILS)
+sumatra: $(SUMATRA_OBJ) ./sumalibs/libsuma.a
-	$(CC) $(LDFLAGS) -o $@ -pthread $(SUMATRA_OBJ) $(LIBFASTAPATH) $(LIBLCSPATH) $(LIBFILEPATH) $(LIBUTILSPATH) $(LIB)
+	$(CC) $(LDFLAGS) -o $@ -pthread $(SUMATRA_OBJ) $(LIBSUMAPATH) $(LIB)
-	
+
 ########
 #
 # project management
@@ -33,12 +36,10 @@ sumatra: $(SUMATRA_OBJ) $(LIBFASTA) $(LIBLCS) $(LIBFILE) $(LIBUTILS)
 ########
 
 clean:
-	rm -f *.o	
+	rm -f $(SUMATRA_OBJ)
-	rm -f *.P
 	rm -f $(EXEC)
-	$(MAKE) -C ./sumalibs/libfasta clean
+	$(MAKE) -C ./sumalibs clean
-	$(MAKE) -C ./sumalibs/liblcs clean
-	$(MAKE) -C ./sumalibs/libfile clean
-	$(MAKE) -C ./sumalibs/libutils clean
 
-		
+install: all
+	install -d $(DESTDIR)$(PREFIX)/bin/
+	install -m 755 $(EXEC) $(DESTDIR)$(PREFIX)/bin/

global.mk

@@ -1,22 +1,15 @@
+LIBSUMAPATH = -L./sumalibs
 
-LIBFASTAPATH = -L./sumalibs/libfasta
+LIBSUMA = ./sumalibs/libsuma.a
-LIBLCSPATH   = -L./sumalibs/liblcs
-LIBFILEPATH  = -L./sumalibs/libfile
-LIBUTILSPATH = -L./sumalibs/libutils
-
-LIBFASTA = ./sumalibs/libfasta/libfasta.a
-LIBLCS   = ./sumalibs/liblcs/liblcs.a
-LIBFILE  = ./sumalibs/libfile/libfile.a
-LIBUTILS = ./sumalibs/libutils/libutils.a
 
 CC=gcc
 LDFLAGS=
 
 
 ifeq ($(CC),gcc)
-        CFLAGS = -O3 -s -DOMP_SUPPORT -fopenmp -w
+        CFLAGS = -I sumalibs -O3 -s -DOMP_SUPPORT -w
 else
-        CFLAGS = -O3 -w
+        CFLAGS = -I sumalibs -O3 -w
 endif
 
 
@@ -32,14 +25,5 @@ default: all
 #
 ########
 
-./sumalibs/libfasta/libfasta.a:
+./sumalibs/libsuma.a:
-	$(MAKE) -C ./sumalibs/libfasta
+	$(MAKE) -C ./sumalibs
-
-./sumalibs/liblcs/liblcs.a:
-	$(MAKE) -C ./sumalibs/liblcs
-
-./sumalibs/libfile/libfile.a:
-	$(MAKE) -C ./sumalibs/libfile
-
-./sumalibs/libutils/libutils.a:
-	$(MAKE) -C ./sumalibs/libutils

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 "1.0.31"
+#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