diff --git a/Makefile b/Makefile index 0f35f0e..fa754e7 100644 --- a/Makefile +++ b/Makefile @@ -51,7 +51,7 @@ all: .activate_module endif -.PHONY: .activate_module +.PHONY: .activate_module .activate_module: git submodule update --init --recursive @@ -60,7 +60,7 @@ endif #modied from htslib makefile -FLAGS = -O3 +FLAGS = -O3 CPPFLAGS := $(filter-out -DNDEBUG,$(CPPFLAGS)) FLAGS2 = $(CPPFLAGS) $(FLAGS) $(LDFLAGS) @@ -100,7 +100,7 @@ version.h: .PHONY: all clean install install-all install-misc misc test -misc: +misc: $(MAKE) -C misc HTSSRC="$(realpath $(HTSSRC))" -include $(OBJ:.o=.d) @@ -121,7 +121,7 @@ metaDMG-cpp: version.h $(OBJ) testclean: rm -f test/acc2taxid.map.gzf570b1db7c.dedup.filtered.rname.bam.bin rm -f test/data/f570b1db7c.dedup.filtered.rname.bam - rm -rf test/output test/logfile version.h + rm -rf test/output test/logfile version.h clean: testclean rm -f *.o *.d $(PROGRAMS) version.h *~ @@ -129,7 +129,7 @@ clean: testclean test: echo "Running unit tests for metaDMG" - cd test;./testAll.sh + cd test;./testAll.sh force: