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|
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
|
