From c4822c487482419821e07b20b913b97398b6abda Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Wed, 27 Mar 2019 17:09:31 +0100
Subject: [PATCH] Cleaner installation

---
 Makefile            | 10 ++++++++--
 mtcompare_sumatra.c |  8 ++++----
 sumalibs            |  2 +-
 sumatra.c           | 10 +++++-----
 sumatra.h           |  2 +-
 5 files changed, 19 insertions(+), 13 deletions(-)

diff --git a/Makefile b/Makefile
index 329af02..8473dad 100644
--- a/Makefile
+++ b/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/
diff --git a/mtcompare_sumatra.c b/mtcompare_sumatra.c
index 2e56f6a..710ef3d 100644
--- a/mtcompare_sumatra.c
+++ b/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 {
diff --git a/sumalibs b/sumalibs
index ed56cb1..b11748e 160000
--- a/sumalibs
+++ b/sumalibs
@@ -1 +1 @@
-Subproject commit ed56cb1d6b1e60a297cd0d1c67a4e17e4c59d202
+Subproject commit b11748eac8b2ff68388d44bcba577323cebe5b08
diff --git a/sumatra.c b/sumatra.c
index d3a3345..daa0689 100644
--- a/sumatra.c
+++ b/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 "1.0.33"
 
 
 /* ----------------------------------------------- */
diff --git a/sumatra.h b/sumatra.h
index d5d6904..d5d5090 100644
--- a/sumatra.h
+++ b/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);