--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/scripts/Makefile	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,96 @@
+#-- Imported variables from top level makefile
+# BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS
+
+ifndef BIN_DIR
+BIN_DIR := $(CURDIR)
+endif
+ifndef AUX_BIN_DIR
+AUX_BIN_DIR := $(CURDIR)
+endif
+ifndef SCRIPT_DIR
+SCRIPT_DIR := $(CURDIR)
+endif
+
+SCRIPT_DIR := $(CURDIR)
+SED := $(filter /%,$(shell /bin/sh -c 'type sed'))
+CSH := $(filter /%,$(shell /bin/sh -c 'type csh'))
+PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
+VPATH := $(BIN_DIR)
+
+ALL := exact-tandems mapview mummerplot nucmer promer \
+       run-mummer1 run-mummer3 nucmer2xfig dnadiff
+
+#-- PHONY rules --#
+.PHONY: all clean
+
+
+all: $(ALL)
+
+
+clean:
+	rm -f *~
+	cd $(BIN_DIR); rm -f $(ALL)
+
+
+
+
+#-- not so PHONY rules --#
+exact-tandems: exact-tandems.csh
+	$(SED)  -e 's?__CSH_PATH?$(CSH)?g' \
+		-e 's?__BIN_DIR?$(BIN_DIR)?g' \
+		-e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+		exact-tandems.csh > $(BIN_DIR)/exact-tandems
+	chmod 755 $(BIN_DIR)/exact-tandems
+
+mapview: mapview.pl
+	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
+		-e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+                mapview.pl > $(BIN_DIR)/mapview
+	chmod 755 $(BIN_DIR)/mapview
+
+mummerplot: mummerplot.pl Foundation.pm
+	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
+                -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+                -e 's?__BIN_DIR?$(BIN_DIR)?g' \
+                mummerplot.pl > $(BIN_DIR)/mummerplot
+	chmod 755 $(BIN_DIR)/mummerplot
+
+dnadiff: dnadiff.pl Foundation.pm
+	$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
+               -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+               -e 's?__BIN_DIR?$(BIN_DIR)?g' \
+                 dnadiff.pl > $(BIN_DIR)/dnadiff
+	chmod 755 $(BIN_DIR)/dnadiff
+
+nucmer: nucmer.pl Foundation.pm
+	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
+                -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+                -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
+                -e 's?__BIN_DIR?$(BIN_DIR)?g' \
+                 nucmer.pl > $(BIN_DIR)/nucmer
+	chmod 755 $(BIN_DIR)/nucmer
+
+promer: promer.pl Foundation.pm
+	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
+                -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+                -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
+                -e 's?__BIN_DIR?$(BIN_DIR)?g' \
+                promer.pl > $(BIN_DIR)/promer
+	chmod 755 $(BIN_DIR)/promer
+
+run-mummer1: run-mummer1.csh
+	$(SED)  -e 's?__CSH_PATH?$(CSH)?g' \
+		-e 's?__BIN_DIR?$(BIN_DIR)?g' \
+		run-mummer1.csh > $(BIN_DIR)/run-mummer1
+	chmod 755 $(BIN_DIR)/run-mummer1
+
+run-mummer3: run-mummer3.csh
+	$(SED)  -e 's?__CSH_PATH?$(CSH)?g' \
+		-e 's?__BIN_DIR?$(BIN_DIR)?g' \
+		run-mummer3.csh > $(BIN_DIR)/run-mummer3
+	chmod 755 $(BIN_DIR)/run-mummer3
+
+nucmer2xfig: nucmer2xfig.pl
+	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
+		nucmer2xfig.pl > $(BIN_DIR)/nucmer2xfig
+	chmod 755 $(BIN_DIR)/nucmer2xfig