jpayne@69: #-- Imported variables from top level makefile
jpayne@69: # BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS
jpayne@69: 
jpayne@69: ifndef BIN_DIR
jpayne@69: BIN_DIR := $(CURDIR)
jpayne@69: endif
jpayne@69: ifndef AUX_BIN_DIR
jpayne@69: AUX_BIN_DIR := $(CURDIR)
jpayne@69: endif
jpayne@69: ifndef SCRIPT_DIR
jpayne@69: SCRIPT_DIR := $(CURDIR)
jpayne@69: endif
jpayne@69: 
jpayne@69: SCRIPT_DIR := $(CURDIR)
jpayne@69: SED := $(filter /%,$(shell /bin/sh -c 'type sed'))
jpayne@69: CSH := $(filter /%,$(shell /bin/sh -c 'type csh'))
jpayne@69: PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
jpayne@69: VPATH := $(BIN_DIR)
jpayne@69: 
jpayne@69: ALL := exact-tandems mapview mummerplot nucmer promer \
jpayne@69:        run-mummer1 run-mummer3 nucmer2xfig dnadiff
jpayne@69: 
jpayne@69: #-- PHONY rules --#
jpayne@69: .PHONY: all clean
jpayne@69: 
jpayne@69: 
jpayne@69: all: $(ALL)
jpayne@69: 
jpayne@69: 
jpayne@69: clean:
jpayne@69: 	rm -f *~
jpayne@69: 	cd $(BIN_DIR); rm -f $(ALL)
jpayne@69: 
jpayne@69: 
jpayne@69: 
jpayne@69: 
jpayne@69: #-- not so PHONY rules --#
jpayne@69: exact-tandems: exact-tandems.csh
jpayne@69: 	$(SED)  -e 's?__CSH_PATH?$(CSH)?g' \
jpayne@69: 		-e 's?__BIN_DIR?$(BIN_DIR)?g' \
jpayne@69: 		-e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
jpayne@69: 		exact-tandems.csh > $(BIN_DIR)/exact-tandems
jpayne@69: 	chmod 755 $(BIN_DIR)/exact-tandems
jpayne@69: 
jpayne@69: mapview: mapview.pl
jpayne@69: 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
jpayne@69: 		-e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
jpayne@69:                 mapview.pl > $(BIN_DIR)/mapview
jpayne@69: 	chmod 755 $(BIN_DIR)/mapview
jpayne@69: 
jpayne@69: mummerplot: mummerplot.pl Foundation.pm
jpayne@69: 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
jpayne@69:                 -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
jpayne@69:                 -e 's?__BIN_DIR?$(BIN_DIR)?g' \
jpayne@69:                 mummerplot.pl > $(BIN_DIR)/mummerplot
jpayne@69: 	chmod 755 $(BIN_DIR)/mummerplot
jpayne@69: 
jpayne@69: dnadiff: dnadiff.pl Foundation.pm
jpayne@69: 	$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
jpayne@69:                -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
jpayne@69:                -e 's?__BIN_DIR?$(BIN_DIR)?g' \
jpayne@69:                  dnadiff.pl > $(BIN_DIR)/dnadiff
jpayne@69: 	chmod 755 $(BIN_DIR)/dnadiff
jpayne@69: 
jpayne@69: nucmer: nucmer.pl Foundation.pm
jpayne@69: 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
jpayne@69:                 -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
jpayne@69:                 -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
jpayne@69:                 -e 's?__BIN_DIR?$(BIN_DIR)?g' \
jpayne@69:                  nucmer.pl > $(BIN_DIR)/nucmer
jpayne@69: 	chmod 755 $(BIN_DIR)/nucmer
jpayne@69: 
jpayne@69: promer: promer.pl Foundation.pm
jpayne@69: 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
jpayne@69:                 -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
jpayne@69:                 -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
jpayne@69:                 -e 's?__BIN_DIR?$(BIN_DIR)?g' \
jpayne@69:                 promer.pl > $(BIN_DIR)/promer
jpayne@69: 	chmod 755 $(BIN_DIR)/promer
jpayne@69: 
jpayne@69: run-mummer1: run-mummer1.csh
jpayne@69: 	$(SED)  -e 's?__CSH_PATH?$(CSH)?g' \
jpayne@69: 		-e 's?__BIN_DIR?$(BIN_DIR)?g' \
jpayne@69: 		run-mummer1.csh > $(BIN_DIR)/run-mummer1
jpayne@69: 	chmod 755 $(BIN_DIR)/run-mummer1
jpayne@69: 
jpayne@69: run-mummer3: run-mummer3.csh
jpayne@69: 	$(SED)  -e 's?__CSH_PATH?$(CSH)?g' \
jpayne@69: 		-e 's?__BIN_DIR?$(BIN_DIR)?g' \
jpayne@69: 		run-mummer3.csh > $(BIN_DIR)/run-mummer3
jpayne@69: 	chmod 755 $(BIN_DIR)/run-mummer3
jpayne@69: 
jpayne@69: nucmer2xfig: nucmer2xfig.pl
jpayne@69: 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
jpayne@69: 		nucmer2xfig.pl > $(BIN_DIR)/nucmer2xfig
jpayne@69: 	chmod 755 $(BIN_DIR)/nucmer2xfig