Description: use Debian's GenomeTools
Author: Sascha Steinbiss <satta@debian.org>
--- a/Makefile
+++ b/Makefile
@@ -15,19 +15,17 @@
 # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 #
 
-INCLUDEOPT:=-I$(CURDIR)/../genometools/src \
-            -I$(CURDIR)/../genometools/src/external/zlib-1.2.8 \
-            -I$(CURDIR)/../genometools/src/external/bzip2-1.0.6 \
-            -I$(CURDIR)/../genometools/src/external/expat-2.0.1/lib \
-            -I$(CURDIR)/../genometools/src/external/lua-5.1.5/src \
+INCLUDEOPT:=-I/usr/include/genometools \
+	    -I/usr/include/vmatch \
+	    -I/usr/include/lua5.1 \
             -I$(CURDIR)/src -I$(CURDIR)/obj \
 # these variables are exported by the configuration script
-CC:=gcc
+#CC:=gcc
 CXX:=g++
 EXP_CFLAGS:=$(CFLAGS)
 EXP_CXXFLAGS:=$(CXXFLAGS)
 EXP_CPPFLAGS:=$(CPPFLAGS)
-EXP_LDLIBS:=$(LIBS) -lm
+EXP_LDLIBS:=$(LIBS) -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1
 
 ifneq ($(fpic),no)
   FPIC:=-fPIC
@@ -130,11 +128,11 @@
 GTMAIN_DEP:=$(GTMAIN_SRC:%.c=obj/%.d)
 
 VSTREEDIR:=../vstree/src
-GTHLIBS:=$(VSTREEDIR)/lib/$(CONFIGGUESS)/$(BIT)/libvmatch.a\
-         $(VSTREEDIR)/lib/$(CONFIGGUESS)/$(BIT)/libvmengine.a\
-         $(VSTREEDIR)/lib/$(CONFIGGUESS)/$(BIT)/libmkvtree.a\
-         $(VSTREEDIR)/lib/$(CONFIGGUESS)/$(BIT)/libkurtz.a\
-         $(VSTREEDIR)/lib/$(CONFIGGUESS)/$(BIT)/libkurtz-basic.a
+GTHLIBS:=/usr/lib/libvmatch.a\
+         /usr/lib/libvmengine.a\
+         /usr/lib/libmkvtree.a\
+         /usr/lib/libkurtz.a\
+         /usr/lib/libkurtz-basic.a
 GTH_CPPFLAGS+=-I$(CURDIR)/$(VSTREEDIR)/include \
              -I$(CURDIR)/$(VSTREEDIR)/Vmatch \
 
@@ -209,7 +207,7 @@
 all: lib/libgenomethreader.a bin/gth bin/gthconsensus bin/gthbssmfileinfo \
      bin/gthbssmbuild bin/gthbssmprint bin/gthbssmrmsd bin/gthbssmtrain \
      bin/gthfilestat bin/gthmkbssmfiles bin/gthsplit bin/gthunit \
-     bin/gthgetseq bin/align_dna bin/rnv
+     bin/gthgetseq bin/align_dna
 
 lib/libgenomethreader.a: obj/gth_config.h $(LIBGENOMETHREADER_OBJ)
 	@echo "[link $(@F)]"
@@ -231,67 +229,67 @@
 $(1): $(2)
 	@echo "[link $$(@F)]"
 	@test -d $$(@D) || mkdir -p $$(@D)
-	@$$(CC) $$(LDFLAGS) $$(GTH_LDFLAGS) $$(filter-out $$(OVERRIDELIBS),$$^) \
+	$$(CC) $$(LDFLAGS) $$(GTH_LDFLAGS) $$(filter-out $$(OVERRIDELIBS),$$^) \
 	  $$(filter-out $$(patsubst lib%.a,-l%,$$(notdir $$(OVERRIDELIBS))),\
 	  $$(EXP_LDLIBS)) $$(OVERRIDELIBS) -o $$@
 endef
 
 $(eval $(call PROGRAM_template, bin/gth, obj/src/gth.o \
                                 lib/libgenomethreader.a \
-                                $(GTHLIBS) ../genometools/lib/libgenometools.a))
+                                $(GTHLIBS)))
 
 $(eval $(call PROGRAM_template, bin/gthconsensus, obj/src/gthconsensus.o \
                                 lib/libgenomethreader.a \
-                                $(GTHLIBS) ../genometools/lib/libgenometools.a))
+                                $(GTHLIBS)))
 
 $(eval $(call PROGRAM_template, bin/gthbssmfileinfo, obj/src/gthbssmfileinfo.o \
                                 lib/libgenomethreader.a \
-                                ../genometools/lib/libgenometools.a $(GTHLIBS)))
+                                $(GTHLIBS)))
 
 $(eval $(call PROGRAM_template, bin/gthbssmbuild, obj/src/gthbssmbuild.o \
                                 lib/libgenomethreader.a \
-                                ../genometools/lib/libgenometools.a $(GTHLIBS)))
+                                $(GTHLIBS)))
 
 $(eval $(call PROGRAM_template, bin/gthbssmprint, obj/src/gthbssmprint.o \
                                 lib/libgenomethreader.a \
-                                ../genometools/lib/libgenometools.a $(GTHLIBS)))
+                                $(GTHLIBS)))
 
 $(eval $(call PROGRAM_template, bin/gthbssmrmsd, obj/src/gthbssmrmsd.o \
                                 lib/libgenomethreader.a \
-                                ../genometools/lib/libgenometools.a $(GTHLIBS)))
+                                $(GTHLIBS)))
 
 $(eval $(call PROGRAM_template, bin/gthbssmtrain, obj/src/gthbssmtrain.o \
                                 lib/libgenomethreader.a \
-                                ../genometools/lib/libgenometools.a $(GTHLIBS)))
+                                $(GTHLIBS)))
 
 $(eval $(call PROGRAM_template, bin/gthfilestat, obj/src/gthfilestat.o \
                                 lib/libgenomethreader.a \
-                                $(GTHLIBS) ../genometools/lib/libgenometools.a))
+                                $(GTHLIBS)))
 
 $(eval $(call PROGRAM_template, bin/gthmkbssmfiles, obj/src/gthmkbssmfiles.o \
                                 lib/libgenomethreader.a \
-                                $(GTHLIBS) ../genometools/lib/libgenometools.a))
+                                $(GTHLIBS)))
 
 $(eval $(call PROGRAM_template, bin/gthsplit, obj/src/gthsplit.o \
                                 lib/libgenomethreader.a \
-                                $(GTHLIBS) ../genometools/lib/libgenometools.a))
+                                $(GTHLIBS)))
 
 $(eval $(call PROGRAM_template, bin/gthunit, obj/src/gthunit.o \
                                 lib/libgenomethreader.a \
-                                $(GTHLIBS) ../genometools/lib/libgenometools.a))
+                                $(GTHLIBS)))
 
 $(eval $(call PROGRAM_template, bin/gthgetseq, obj/src/gthgetseq.o \
                                 lib/libgenomethreader.a \
-                                ../genometools/lib/libgenometools.a $(GTHLIBS)))
+                                $(GTHLIBS)))
 
 $(eval $(call PROGRAM_template, bin/align_dna, obj/src/align_dna.o \
                                 lib/libgenomethreader.a \
-                                ../genometools/lib/libgenometools.a $(GTHLIBS)))
+                                $(GTHLIBS)))
 
-bin/rnv: $(RNVMAIN_OBJ) lib/librnv.a ../genometools/lib/libexpat.a
-	@echo "[link $(@F)]"
-	@test -d $(@D) || mkdir -p $(@D)
-	@$(CC) $(EXP_LDFLAGS) $(GTH_LDFLAGS) $^ -o $@
+#bin/rnv: $(RNVMAIN_OBJ) lib/librnv.a ../genometools/lib/libexpat.a
+#	@echo "[link $(@F)]"
+#	@test -d $(@D) || mkdir -p $(@D)
+#	@$(CC) $(EXP_LDFLAGS) $(GTH_LDFLAGS) $^ -o $@
 
 obj/gth_config.h: VERSION
 	@echo '[create $@]'
@@ -321,9 +319,9 @@
 $(1): $(2)
 	@echo "[compile $$(@F)]"
 	@test -d $$(@D) || mkdir -p $$(@D)
-	@$$(CC) -c $$< -o $$@ $$(EXP_CPPFLAGS) $$(GTH_CPPFLAGS) $$(EXP_CFLAGS) \
+	$$(CC) -c $$< -o $$@ $$(EXP_CPPFLAGS) $$(GTH_CPPFLAGS) $$(EXP_CFLAGS) \
 	  $$(GTH_CFLAGS) $(3)
-	@$$(CC) -c $$< -o $$(@:.o=.d) $$(EXP_CPPFLAGS) $$(GTH_CPPFLAGS) \
+	$$(CC) -c $$< -o $$(@:.o=.d) $$(EXP_CPPFLAGS) $$(GTH_CPPFLAGS) \
         $(3) -MM -MP -MT $$@
 endef
 
@@ -332,17 +330,17 @@
 obj/%.o: %.cxx
 	@echo "[compile $(@F)]"
 	@test -d $(@D) || mkdir -p $(@D)
-	@$(CXX) -c $< -o $@ $(EXP_CPPFLAGS) $(GTH_CPPFLAGS) \
+	$(CXX) -c $< -o $@ $(EXP_CPPFLAGS) $(GTH_CPPFLAGS) \
 	  $(EXP_CXXFLAGS) $(GTH_CXXFLAGS)
-	@$(CXX) -c $< -o $(@:.o=.d) $(EXP_CPPFLAGS) $(GTH_CPPFLAGS) -MM -MP \
+	$(CXX) -c $< -o $(@:.o=.d) $(EXP_CPPFLAGS) $(GTH_CPPFLAGS) -MM -MP \
 	  -MT $@
 
 obj/%.o: %.cpp
 	@echo "[compile $@]"
 	@test -d $(@D) || mkdir -p $(@D)
-	@$(CXX) -c $< -o $@ $(EXP_CPPFLAGS) $(GTH_CPPFLAGS) \
+	$(CXX) -c $< -o $@ $(EXP_CPPFLAGS) $(GTH_CPPFLAGS) \
 	  $(EXP_CXXFLAGS) $(GTH_CXXFLAGS)
-	@$(CXX) -c $< -o $(@:.o=.d) $(EXP_CPPFLAGS) $(GTH_CPPFLAGS) -MM -MP \
+	$(CXX) -c $< -o $(@:.o=.d) $(EXP_CPPFLAGS) $(GTH_CPPFLAGS) -MM -MP \
 	  -MT $@
 
 obj/src/core/versionfunc.o: obj/gth_config.h
