debian/patches/hardening.patch

@@ -4,7 +4,7 @@ Last-Update: Tue, 04 Dec 2018 08:36:52 +0100
 
 --- a/src/Makefile
 +++ b/src/Makefile
-@@ -1,6 +1,6 @@
+@@ -1,54 +1,54 @@
  CC = gcc $(CFLAGS)
  CPP = g++ $(CFLAGS)
 -CFLAGS = -O3 # -Wall -W
@@ -12,7 +12,9 @@ Last-Update: Tue, 04 Dec 2018 08:36:52 +0100
  TRGT_DIR = ..
  
  all: ../anchors ../chaos ../order ../mlagan ../prolagan ../utils/bin2mf ../utils/bin2bl ../utils/cextract ../utils/cstat ../utils/contigorder ../utils/getbounds ../utils/getlength ../utils/getoverlap ../utils/rc ../utils/seqmerge ../utils/scorealign ../utils/scorecontigs ../utils/getcontigpos ../utils/fa2xfa ../utils/Glue ../utils/dotplot ../utils/overlay
-@@ -9,46 +9,46 @@ clean:
+-	(cd glocal; $(MAKE))
++	(cd glocal; $(MAKE) LDFLAGS=$(LDFLAGS))
+ clean: 
  	rm -f *.o *~ utils/*~ mlagan.purify core
  	(cd glocal; $(MAKE) clean)
  ../anchors: anchors.c skiplist.c
@@ -81,3 +83,22 @@ Last-Update: Tue, 04 Dec 2018 08:36:52 +0100
  ../utils/dotplot: utils/dotplot.cpp
 -	$(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
 +	$(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp $(LDFLAGS)
+--- a/src/glocal/Makefile
++++ b/src/glocal/Makefile
+@@ -1,6 +1,6 @@
+ CC = g++
+ OPTFLAGS = 
+-CFLAGS = $(OPTFLAGS) -O3
++CFLAGS += $(OPTFLAGS) -O3
+ CLINKER = g++ 
+ # LIBDIR = -L/usr/local/lib
+ MLIB =  -lm
+@@ -10,7 +10,7 @@ TRGT = glocal
+ OBJECTS = glocal.o io.o rightinfluence.o leftinfluence.o score.o
+ 
+ .cpp.o:
+-	$(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp
++	$(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp $(LDFLAGS)
+ 
+ $(TRGT): $(OBJECTS)
+ 	$(CLINKER) $(OPTFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)

debian/rules

@@ -11,3 +11,7 @@ override_dh_auto_build:
 override_dh_auto_clean:
 	dh_auto_clean
 	rm -f prolagan
+
+override_dh_fixperms:
+	dh_fixperms
+	find debian -name flipchaos.pl -exec chmod +x \{\} \;