Makefile

+PREFIX=/usr/local
+
+CFLAGS=-I$(PREFIX)/include
+
 EXEC = sumatra
 
 SUMATRA_SRC = sumatra.c \
@@ -5,10 +9,9 @@ SUMATRA_SRC= sumatra.c \
 			              
 SUMATRA_OBJ = $(patsubst %.c,%.o,$(SUMATRA_SRC))
 
-
 SRCS = $(SUMATRA_SRC)
 
-LIB= -lfasta -llcs -lfile -lutils -lz -lm
+LIB = -lsuma -lz -lm
 
 include ./global.mk
 
@@ -23,8 +26,8 @@ all: $(EXEC)
 
 # executable compilation and link
 
-sumatra: $(SUMATRA_OBJ) $(LIBFASTA) $(LIBLCS) $(LIBFILE) $(LIBUTILS)
-	$(CC) $(LDFLAGS) -o $@ -pthread $(SUMATRA_OBJ) $(LIBFASTAPATH) $(LIBLCSPATH) $(LIBFILEPATH) $(LIBUTILSPATH) $(LIB)
+sumatra: $(SUMATRA_OBJ)
+	$(CC) $(LDFLAGS) -o $@ -pthread $(SUMATRA_OBJ) $(LIBSUMAPATH) $(LIB)
 	
 ########
 #
@@ -33,12 +36,10 @@ sumatra: $(SUMATRA_OBJ) $(LIBFASTA) $(LIBLCS) $(LIBFILE) $(LIBUTILS)
 ########
 
 clean:
-	rm -f *.o	
-	rm -f *.P
+	rm -f $(SUMATRA_OBJ)	
 	rm -f $(EXEC)
-	$(MAKE) -C ./sumalibs/libfasta clean
-	$(MAKE) -C ./sumalibs/liblcs clean
-	$(MAKE) -C ./sumalibs/libfile clean
-	$(MAKE) -C ./sumalibs/libutils clean
-
+	$(MAKE) -C ./sumalibs clean
 
+install: all
+	install -d $(DESTDIR)$(PREFIX)/bin/
+	install -m 755 $(EXEC) $(DESTDIR)$(PREFIX)/bin/

README.md

+[See the wiki](https://git.metabarcoding.org/obitools/sumatra/wikis/home)
\ No newline at end of file

debian/changelog

+sumatra (1.0.34-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * debhelper 12
+  * Standards-Version: 4.3.0
+  TODO: https://github.com/mesocentrefc/sumatra
+
+ -- Andreas Tille <tille@debian.org>  Tue, 09 Jul 2019 15:45:27 +0200
+
 sumatra (1.0.31-2) unstable; urgency=medium
 
   * debhelper 11

debian/compat

-11
+12

debian/control

@@ -4,8 +4,8 @@ Uploaders: Tim Booth <tbooth@ceh.ac.uk>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~)
-Standards-Version: 4.2.1
+Build-Depends: debhelper (>= 12~)
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/sumatra
 Vcs-Git: https://salsa.debian.org/med-team/sumatra.git
 Homepage: http://metabarcoding.org/sumatra

debian/patches/hardening.patch

@@ -4,8 +4,8 @@ Description: Propagate hardening options
 
 --- a/global.mk
 +++ b/global.mk
-@@ -10,7 +10,7 @@ LIBFILE  = ./sumalibs/libfile/libfile.a
- LIBUTILS = ./sumalibs/libutils/libutils.a
+@@ -4,7 +4,7 @@ LIBSUMAPATH = -L./sumalibs
+ LIBSUMA = ./sumalibs/libsuma.a
  
  CC=gcc
 -LDFLAGS=

debian/patches/no_zlib.patch

-Author: Tim Booth <tbooth@ceh.ac.uk>
-Last-Update: Fri, 13 Feb 2015 16:24:17 +0000
-Description There is no actual use of Zlib, so no need to build against it.
-
---- a/Makefile
-+++ b/Makefile
-@@ -8,7 +8,7 @@ SUMATRA_OBJ= $(patsubst %.c,%.o,$(SUMATR
- 
- SRCS= $(SUMATRA_SRC)
- 
--LIB= -lfasta -llcs -lfile -lutils -lz -lm
-+LIB= -lfasta -llcs -lfile -lutils -lm
- 
- include ./global.mk
- 

debian/patches/series

 hardening.patch
-no_zlib.patch

global.mk

 
-LIBFASTAPATH = -L./sumalibs/libfasta
-LIBLCSPATH   = -L./sumalibs/liblcs
-LIBFILEPATH  = -L./sumalibs/libfile
-LIBUTILSPATH = -L./sumalibs/libutils
+LIBSUMAPATH = -L./sumalibs
 
-LIBFASTA = ./sumalibs/libfasta/libfasta.a
-LIBLCS   = ./sumalibs/liblcs/liblcs.a
-LIBFILE  = ./sumalibs/libfile/libfile.a
-LIBUTILS = ./sumalibs/libutils/libutils.a
+LIBSUMA = ./sumalibs/libsuma.a
 
 CC=gcc
 LDFLAGS=
 
 
 ifeq ($(CC),gcc)
-        CFLAGS = -O3 -s -DOMP_SUPPORT -fopenmp -w
+        CFLAGS = -O3 -s -DOMP_SUPPORT -w
 else
         CFLAGS = -O3 -w
 endif
@@ -32,14 +26,5 @@ default: all
 #
 ########
 
-./sumalibs/libfasta/libfasta.a:
-	$(MAKE) -C ./sumalibs/libfasta
-
-./sumalibs/liblcs/liblcs.a:
-	$(MAKE) -C ./sumalibs/liblcs
-
-./sumalibs/libfile/libfile.a:
-	$(MAKE) -C ./sumalibs/libfile
-
-./sumalibs/libutils/libutils.a:
-	$(MAKE) -C ./sumalibs/libutils
\ No newline at end of file
+./sumalibs/libsuma.a:
+	$(MAKE) -C ./sumalibs

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 {