Applying contributed patches for various makefiles

dubeyshubham108 · Dec 16, 2010 · fa72953 · fa72953
1 parent ab0e202
commit fa72953
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Showing 6 changed files with 64 additions and 30 deletions.
diff --git a/cad/Makefile.am b/cad/Makefile.am
@@ -3,7 +3,7 @@ SUBDIRS = src doc partlib plugins
 
 install-exec-hook:
 	@echo Installing license files...
-	cp -R Licenses $(pkgdatadir)-$(PACKAGE_VERSION)/
+#	cp -R Licenses $(pkgdatadir)-$(PACKAGE_VERSION)/
 
 dist-hook:
 	mkdir $(distdir)/Licenses

diff --git a/cad/doc/Makefile.am b/cad/doc/Makefile.am
@@ -3,7 +3,7 @@ EXTRA_DIST = keyboardshortcuts.htm mousecontrols.htm
 
 install-exec-hook:
 	@echo Copying the UI documentation files...
-	mkdir -p $(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/doc
-	cp keyboardshortcuts.htm $(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/doc/
-	cp mousecontrols.htm $(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/doc/
+	mkdir -p $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/doc
+	cp keyboardshortcuts.htm $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/doc/
+	cp mousecontrols.htm $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/doc/
 
diff --git a/cad/plugins/DNA/Makefile.am b/cad/plugins/DNA/Makefile.am
@@ -1,8 +1,8 @@
 
 install-exec-hook:
 	@echo Installing DNA Generator plugin...
-	mkdir -p $(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/plugins/DNA
-	cp -R * $(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/plugins/DNA/
+	mkdir -p $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/plugins/DNA
+	cp -R * $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/plugins/DNA/
 
 dist-hook:
 	cp -R * $(distdir)/

diff --git a/cad/plugins/GROMACS/gromacs-3.3.2/src/tools/Makefile.am b/cad/plugins/GROMACS/gromacs-3.3.2/src/tools/Makefile.am
@@ -69,7 +69,7 @@ LDADD = $(lib_LTLIBRARIES) ../mdlib/libmd@[email protected] \
 install-exec-hook:
 	libname="libgmxana@LIBSUFFIX@"; \
 	nompi="`echo $$libname | sed -e 's,_mpi,,'`"; \
-	libdir="$(libdir)"; \
+	libdir="$(DESTDIR)/$(libdir)"; \
 	if echo $$libname | grep mpi >/dev/null ; then \
 	  (cd $$libdir && test -e $$libname.a -a ! -e $$nompi.a && $(LN_S) $$libname.a $$nompi.a ; exit 0); \
 	  (cd $$libdir && test -e $$libname.so -a ! -e $$nompi.so && $(LN_S) $$libname.so $$nompi.so ; exit 0); \

diff --git a/cad/src/Makefile.am b/cad/src/Makefile.am
@@ -11,40 +11,69 @@ else
 endif
 
 install-exec-hook:
-	mkdir -p $(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	mkdir -p $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
 
 if RUN_FREEZEPYTHON
 	@echo Installing the frozen NanoEngineer-1...
-	cp -r dist/* $(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program/
-	echo '#!/bin/sh' > $(bindir)/NanoEngineer-$(PACKAGE_VERSION)
-	echo $(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program/NanoEngineer-1 >> $(bindir)/NanoEngineer-$(PACKAGE_VERSION)
+	cp -r dist/* $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program/
+	echo '#!/bin/sh' > $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION)
+	echo $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program/NanoEngineer-1 >> $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION)
 else
 	@echo Installing byte-compiled NanoEngineer-1...
-	cp *.pyc $(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program/
-	mkdir -p $(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program/exprs
-	cp exprs/*.pyc $(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program/exprs/
-	mkdir -p $(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program/PM
-	cp PM/*.pyc $(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program/PM/
-	echo '#!/bin/sh' > $(bindir)/NanoEngineer-$(PACKAGE_VERSION)
-	echo python $(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program/main.pyc >> $(bindir)/NanoEngineer-$(PACKAGE_VERSION)
+	cp *.pyc $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program/
+	cp -r analysis $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r cnt $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r commandSequencer $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r commandToolbar $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r command_support $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r commands $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r dna $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r exprs $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r files $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r foundation $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r geometry $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r graphics $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r history $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r model $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r modelTree $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r model_updater $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r ne1_startup $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r ne1_ui $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r operations $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r outtakes $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r platform_dependent $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r PM $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r processes $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r protein $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r prototype $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r scratch $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r simulation $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r sponsors $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r temporary_commands $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r tests $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r tools $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r utilities $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	cp -r widgets $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program
+	echo '#!/bin/sh' > $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION)
+	echo PYTHONPATH=$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program python $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/program/main.pyc >> $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION)
 endif
-	chmod 755 $(bindir)/NanoEngineer-$(PACKAGE_VERSION)
-	pushd $(bindir) && rm -f NanoEngineer-1
-	pushd $(bindir) && ln -s NanoEngineer-$(PACKAGE_VERSION) NanoEngineer-1
-#	rm -f $(bindir)/NanoEngineer-1
-#	ln -s $(bindir)/NanoEngineer-$(PACKAGE_VERSION) $(bindir)/NanoEngineer-1
+	chmod 755 $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION)
+	pushd $(DESTDIR)/$(bindir) && rm -f NanoEngineer-1
+	pushd $(DESTDIR)/$(bindir) && ln -s NanoEngineer-$(PACKAGE_VERSION) NanoEngineer-1
+#	rm -f $(DESTDIR)/$(bindir)/NanoEngineer-1
+#	ln -s $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION) $(DESTDIR)/$(bindir)/NanoEngineer-1
 
 	@echo Copying the GAMESS helper script...
-	mkdir -p $(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/bin
-	cp rungms $(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/bin/
+#	mkdir -p $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/bin
+#	cp rungms $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/bin/
 
 	@echo Copying images...
-	mkdir -p $(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/src
-	cp -R ui $(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/src/
+	mkdir -p $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/src
+	cp -R ui $(DESTDIR)/$(bindir)/NanoEngineer-$(PACKAGE_VERSION).app/src/
 
 	@echo Copying ReadMe.html...
-	mkdir -p $(pkgdatadir)-$(PACKAGE_VERSION)
-	cp ReadMe.html $(pkgdatadir)-$(PACKAGE_VERSION)/
+	mkdir -p $(DESTDIR)/$(pkgdatadir)-$(PACKAGE_VERSION)
+	cp ReadMe.html $(DESTDIR)/$(pkgdatadir)-$(PACKAGE_VERSION)/
 
 EXTRA_DIST = ReadMe.html rungms
 

diff --git a/sim/src/Makefile.am b/sim/src/Makefile.am
@@ -14,6 +14,7 @@ sim_la_LDFLAGS = -module
 
 sim_la_SOURCES = \
 	allocate.c allocate.h \
+	amber_patterns.c amber_patterns.h \
 	debug.h \
 	dynamics.c dynamics.h \
 	globals.c globals.h \
@@ -24,9 +25,13 @@ sim_la_SOURCES = \
 	minimize.c minimize.h \
 	minstructure.c minstructure.h \
 	newtables.c newtables.h \
+	pam5_patterns.c pam5_patterns.h \
+	pattern.c pattern.h \
 	part.c part.h \
 	potential.c potential.h \
+	printGromacsTopology.c printGromacsTopology.h \
 	printers.c printers.h \
+	read_amber_itp.c read_amber_itp.h \
 	readmmp.c readmmp.h \
 	readxyz.c readxyz.h \
 	rigid.c rigid.h \
@@ -49,7 +54,7 @@ version.h:
 	python makehelp.py "$(CFLAGS)" "$(LDFLAGS)" "@UNAME_A@" \
 		| grep -v "^running " > version.h
 sim.c: sim.pyx simhelp.c
-	@PYREXC@ sim.pyx
+	pyrexc sim.pyx
 
 EXTRA_DIST = \
 	stretch.py stretch.parms bend.py bending.parms makehelp.py sim.pyx \