Author: Andreas Tille <tille@debian.org>
Last-Update: Wed, 24 Mar 2010 17:10:43 +0000
Bug-Debian: http://bugs.debian.org/575105
Description: Make sure scripts will use the installation path instead of
 the temporary build path

--- MUMmer3.22.orig/scripts/Makefile
+++ MUMmer3.22/scripts/Makefile
@@ -4,14 +4,19 @@
 ifndef BIN_DIR
 BIN_DIR := $(CURDIR)
 endif
+ifndef INSTALL_BIN_DIR
+FINAL_BIN_DIR := $(BIN_DIR)
+endif
 ifndef AUX_BIN_DIR
 AUX_BIN_DIR := $(CURDIR)
 endif
+ifndef INSTALL_AUX_BIN_DIR
+FINAL_AUX_BIN_DIR := $(BIN_DIR)
+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'))
@@ -35,59 +40,52 @@
 
 
 #-- 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
+exact-tandems: ../debian/sh-replacement-scripts/exact-tandems
+	cp -a $^ $(BIN_DIR)
 	chmod 755 $(BIN_DIR)/exact-tandems
 
 mapview: mapview.pl
 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
-		-e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+		-e 's?__SCRIPT_DIR?$(FINAL_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' \
+                -e 's?__SCRIPT_DIR?$(FINAL_SCRIPT_DIR)?g' \
+                -e 's?__BIN_DIR?$(FINAL_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' \
+               -e 's?__SCRIPT_DIR?$(FINAL_SCRIPT_DIR)?g' \
+               -e 's?__BIN_DIR?$(FINAL_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?$(BIN_DIR)?g' \
+                -e 's?__SCRIPT_DIR?$(FINAL_SCRIPT_DIR)?g' \
+                -e 's?__AUX_BIN_DIR?$(FINAL_AUX_BIN_DIR)?g' \
+                -e 's?__BIN_DIR?$(FINAL_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?$(BIN_DIR)?g' \
+                -e 's?__SCRIPT_DIR?$(FINAL_SCRIPT_DIR)?g' \
+                -e 's?__AUX_BIN_DIR?$(FINAL_AUX_BIN_DIR)?g' \
+                -e 's?__BIN_DIR?$(FINAL_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
+run-mummer1: ../debian/sh-replacement-scripts/run-mummer1
+	cp -a $^ $(BIN_DIR)
 	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
+run-mummer3: ../debian/sh-replacement-scripts/run-mummer3
+	cp -a $^ $(BIN_DIR)
 	chmod 755 $(BIN_DIR)/run-mummer3
 
 nucmer2xfig: nucmer2xfig.pl