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# BIOCHAM system http://contraintes.inria.fr/BIOCHAM/
# Copyright 2003-2010, INRIA, Projet Contraintes
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
# 
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
# 
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
#
# Makefile.am
# 
# put independent files in biocham_SOURCES
# put files necessary to get biocham.o (i.e. files included by biocham.pl) in
# PLFILES



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bin_SCRIPTS = @GUIBINS@
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installdirs: installdirs-recursive
installdirs-am:
	for dir in "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)" "$(DESTDIR)$(man1dir)" "$(DESTDIR)$(appsdir)" "$(DESTDIR)$(mimedir)" "$(DESTDIR)$(pixmapsdir)" "$(DESTDIR)$(sharedmimedir)"; do \
	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
	done
install: $(BUILT_SOURCES)
	$(MAKE) $(AM_MAKEFLAGS) install-recursive
install-exec: install-exec-recursive
install-data: install-data-recursive
uninstall: uninstall-recursive

install-am: all-am
	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am

installcheck: installcheck-recursive
install-strip:
	if test -z '$(STRIP)'; then \
	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
	      install; \
	else \
	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
	    "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
	fi
mostlyclean-generic:

clean-generic:
	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)

distclean-generic:
	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)

maintainer-clean-generic:
	@echo "This command is intended for maintainers to use"
	@echo "it deletes files that may require special tools to rebuild."
	-test -z "$(BUILT_SOURCES)" || rm -f $(BUILT_SOURCES)
clean: clean-recursive

clean-am: clean-binPROGRAMS clean-generic mostlyclean-am

distclean: distclean-recursive
	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
	-rm -rf ./$(DEPDIR)
	-rm -f Makefile
distclean-am: clean-am distclean-compile distclean-generic \
	distclean-tags

dvi: dvi-recursive

dvi-am:

html: html-recursive

html-am:

info: info-recursive

info-am:

install-data-am: install-dist_appsDATA install-dist_mimeDATA \
	install-dist_pixmapsDATA install-dist_sharedmimeDATA \
	install-man
	@$(NORMAL_INSTALL)
	$(MAKE) $(AM_MAKEFLAGS) install-data-hook
install-dvi: install-dvi-recursive

install-dvi-am:

install-exec-am: install-binPROGRAMS install-binSCRIPTS

install-html: install-html-recursive

install-html-am:

install-info: install-info-recursive

install-info-am:

install-man: install-man1

install-pdf: install-pdf-recursive

install-pdf-am:

install-ps: install-ps-recursive

install-ps-am:

installcheck-am:

maintainer-clean: maintainer-clean-recursive
	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
	-rm -rf $(top_srcdir)/autom4te.cache
	-rm -rf ./$(DEPDIR)
	-rm -f Makefile
maintainer-clean-am: distclean-am maintainer-clean-generic

mostlyclean: mostlyclean-recursive

mostlyclean-am: mostlyclean-compile mostlyclean-generic

pdf: pdf-recursive

pdf-am:

ps: ps-recursive

ps-am:

uninstall-am: uninstall-binPROGRAMS uninstall-binSCRIPTS \
	uninstall-dist_appsDATA uninstall-dist_mimeDATA \
	uninstall-dist_pixmapsDATA uninstall-dist_sharedmimeDATA \
	uninstall-man
	@$(NORMAL_INSTALL)
	$(MAKE) $(AM_MAKEFLAGS) uninstall-hook
uninstall-man: uninstall-man1

.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) all check \
	ctags-recursive install install-am install-data-am \
	install-strip tags-recursive uninstall-am

.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
	all all-am all-local am--refresh check check-am clean \
	clean-binPROGRAMS clean-generic ctags ctags-recursive dist \
	dist-all dist-bzip2 dist-gzip dist-hook dist-lzip dist-lzma \
	dist-shar dist-tarZ dist-xz dist-zip distcheck distclean \
	distclean-compile distclean-generic distclean-tags \
	distcleancheck distdir distuninstallcheck dvi dvi-am html \
	html-am info info-am install install-am install-binPROGRAMS \
	install-binSCRIPTS install-data install-data-am \
	install-data-hook install-dist_appsDATA install-dist_mimeDATA \
	install-dist_pixmapsDATA install-dist_sharedmimeDATA \
	install-dvi install-dvi-am install-exec install-exec-am \
	install-html install-html-am install-info install-info-am \
	install-man install-man1 install-pdf install-pdf-am install-ps \
	install-ps-am install-strip installcheck installcheck-am \
	installdirs installdirs-am maintainer-clean \
	maintainer-clean-generic mostlyclean mostlyclean-compile \
	mostlyclean-generic pdf pdf-am ps ps-am tags tags-recursive \
	uninstall uninstall-am uninstall-binPROGRAMS \
	uninstall-binSCRIPTS uninstall-dist_appsDATA \
	uninstall-dist_mimeDATA uninstall-dist_pixmapsDATA \
	uninstall-dist_sharedmimeDATA uninstall-hook uninstall-man \
	uninstall-man1


@SET_MAKE@
export RM = rm -f

.PHONY: deb minicheck BiochamGUI

biocham.o : $(PLFILES)

biochamAnalyze.o : biochamAnalyze.pl biocham_gsa.c fss.c fss_biocham.c ppl_biocham.c
	"$(GPLC)" -c $(GPLCFLAGS) $^

spawn_redirect.o : spawn_redirect.pl spawn_redirect_c.c
	"$(GPLC)" -c $(GPLCFLAGS) $^

.pl.o:
	"$(GPLC)" -c $(GPLCFLAGS) $<

.c.o:
	"$(GPLC)" -c $(GPLCFLAGS) $<

ChangeLog :
	svn -v log > $@

biocham.1: biocham.pl biochamVars.pl biosyntax.pl
	-$(HELP2MAN) --output=$@ -N ./biocham

biosyntax.pl: biosyntax.pl.in DOC/manual.tex BuildBiosyntax.java
	"$(JAVAC)" -cp ./lib/gson-2.3.1.jar BuildBiosyntax.java
	java -cp .:./lib/gson-2.3.1.jar BuildBiosyntax
	$(RM) BuildBiosyntax*.class

deb: dist
	cp $(distdir).tar.gz ../$(subst B,b,$(PACKAGE))_$(VERSION).orig.tar.gz
	dpkg-buildpackage -rfakeroot -i'.*(png|o)'
	mv ../$(subst B,b,$(PACKAGE))_$(VERSION)* .

biocham_gui: biocham_gui.in Makefile
	sed -e 's,@datadir\@,$(pkgdatadir),g' -e 's,@JARDIR\@,$(JARDIR),g' $< > $@
	chmod a+x $@

minicheck: $(bin_PROGRAMS)
	for file in EXAMPLES/cell_cycle/*.sh EXAMPLES/LEARNING/*/*.sh ; do mv $$file $$file.check; done
	($(MAKE) -C EXAMPLES check && \
		for file in EXAMPLES/cell_cycle/*.sh.check EXAMPLES/LEARNING/*/*.sh.check ; do mv $$file $${file%.check}; done) || \
		(for file in EXAMPLES/cell_cycle/*.sh.check EXAMPLES/LEARNING/*/*.sh.check ; do mv $$file $${file%.check}; done && exit 1)

Biocham.icns : Biocham.tiff
	-tiff2icns $<

Biocham.tiff : Biocham16.tiff Biocham32.tiff Biocham48.tiff Biocham128.tiff
	-tiffutil -cat $^ -out $@

BiochamSetup.exe : biocham.iss biocham.exe BiochamGUI
	rm -Rf .dll
	mkdir .dll
	true # start dot, NuSMV and biocham for 10 sec
	((sleep 10 ; echo "quit") | NuSMV.exe -int &> /dev/null) &
	((sleep 10 ; echo "quit.") | ./biocham.exe &> /dev/null) &
	((sleep 10 ; echo "") | dot.exe &> /dev/null) &
	@true # grab all "modules" used by the running programs and not coming from
	@true # standard places (removed Program Files)
	@true # - uses Mark Russinovich's ListDLLs.exe (http://download.sysinternals.com/files/ListDlls.zip) for Win7
	@true # - uses pv.exe (http://www.teamcti.com/pview/prcview.htm) for WinXP
	@true # both utilities hereinbefore theorically work either on Win7 and WinXP, but pv doesn't see processes launched from shell in MinGW, and Listdlls doesn't give full path of dlls in WinXP
	if [ @EXTRACT_DLL_TOOL@ = pv ] ; then \
	(pv.exe -m NuSMV.exe ; pv.exe -m biocham.exe ; pv.exe -m dot.exe) | grep -i '\.dll' | egrep -iv 'system32|comctl32' | sed -n -e 's/^[^ ]*\.\w* \+\w* \+\w* \+\(.*\)$$/\1/p' | (while read -r dll ; do cp "$$dll" .dll ; done); \
	else \
	(Listdlls.exe NuSMV.exe ; Listdlls.exe biocham.exe ; Listdlls.exe dot.exe) | grep -i '\.dll' | egrep -iv 'system32|comctl32|syswow64|winsxs' | sed -n -e 's/^\w*\s*\w*\s*\(.*\)$$/\1/p' | (while read -r dll ; do cp "$$dll" .dll ; done); \
	fi
	extNuSMV=`which NuSMV.exe` && extNuSMV=`readlink -f "$$extNuSMV"` && cp "$$extNuSMV" .dll # grab NuSMV executable
	extDOT=`which dot.exe` && extDOT=`ls "$$extDOT"`&& extDOT=`readlink -f "$$extDOT"` && cp "$$extDOT" .dll && cp -r "$${extDOT%dot.exe}config6" .dll && mkdir .dll/etc && dot="$${extDOT%bin/dot.exe}" && mkdir .dll/lib&& cp -r "$${dot}lib/pango" .dll/lib # grab dot and some auxiliary files
	sleep 5
	ISCC.exe $< # run InnoSetup

biocham.png : gui/projectImages/SSicon.png
	cp $< $@

Biocham.dmg : biocham Biocham.icns Info.plist PkgInfo gui/biocham.jar dot.sh $(nobase_pkgdata_DATA)
	rm -Rf .Biocham_MacOSX/
	mkdir .Biocham_MacOSX/
	cp -r EXAMPLES .Biocham_MacOSX/
	mkdir -p .Biocham_MacOSX/Biocham.app/Contents/MacOS/
	cp Info.plist PkgInfo .Biocham_MacOSX/Biocham.app/Contents/
	cp /System/Library/Frameworks/JavaVM.framework/Versions/Current/Resources/MacOS/JavaApplicationStub .Biocham_MacOSX/Biocham.app/Contents/MacOS/
	mkdir -p .Biocham_MacOSX/Biocham.app/Contents/Resources/
	cp -r DOC Biocham.icns .Biocham_MacOSX/Biocham.app/Contents/Resources/
	cp biocham .Biocham_MacOSX/Biocham.app/Contents/Resources/biocham.mac
	cp `which NuSMV` .Biocham_MacOSX/Biocham.app/Contents/Resources/NuSMV
	cp dot.sh .Biocham_MacOSX/Biocham.app/Contents/Resources/dot
	for file in `DYLD_PRINT_LIBRARIES=1 ./biocham EXAMPLES/quit.bc 2>&1 | grep '/local/' | cut -d ' ' -f 3`; do cp -f $$file .Biocham_MacOSX/Biocham.app/Contents/Resources/ ; done
	echo "[InternetShortcut]" > .Biocham_MacOSX/Install\ AT\&T\ Graphviz.url
	echo "http://www.graphviz.org/Download_macos.php" >> .Biocham_MacOSX/Install\ AT\&T\ Graphviz.url
	cp biocham.sh .Biocham_MacOSX/Biocham.app/Contents/Resources/biocham
	mkdir -p .Biocham_MacOSX/Biocham.app/Contents/Resources/Java/
	cp gui/*.jar .Biocham_MacOSX/Biocham.app/Contents/Resources/Java/
	cp gui/legacy/*.jar .Biocham_MacOSX/Biocham.app/Contents/Resources/Java/
	ln -s /Applications .Biocham_MacOSX/
# hdiutil create -format UDBZ -scrub -srcfolder .Biocham_MacOSX -volname Biocham -ov Biocham.dmg
	hdiutil create -scrub -srcfolder .Biocham_MacOSX -volname Biocham -ov Biocham.dmg
	hdiutil internet-enable -yes Biocham.dmg
	rm -Rf .Biocham_MacOSX

biocham.tar.gz : biocham gui/biocham.jar
	mkdir -p Biocham/gui
	ldd ./biocham | grep '/local/tools/\|/home' | cut -d' ' -f3 | xargs -n1 -i cp {} Biocham/
	cp biocham biocham_gui Biocham
	cp gui/*.jar Biocham/gui/
	tar -pczf Biocham_x86_64.tar.gz --directory=Biocham .
	rm -rf Biocham/

dist-hook: biocham.tar.gz
	cp -f $(wildcard biocham) $(wildcard *.exe) $(wildcard *.dmg) Biocham_x86_64.tar.gz $(distdir)

install-data-hook :
	-$(UPDMIMEDB) $(sharedmimedir)/..
	-$(UPDDESKDB)

uninstall-hook :
	-$(UPDMIMEDB) $(sharedmimedir)/..
	-$(UPDDESKDB)

spawn_redirect_test: spawn_redirect_test.pl spawn_redirect.pl spawn_redirect_c.c
	"$(GPLC)" $(GPLCFLAGS) --no-top-level -o spawn_redirect_test \
	  spawn_redirect_test.pl spawn_redirect.pl spawn_redirect_c.c

sepi.dll: biocham.o parseXml.o biosyntax.o path.o formal.o spawn_redirect.o biochamTrace.o biochamConserv.o $(PARSING) spawn_redirect_c.c sepi_dassault.c
	"$(GPLC)" -o $@ $(patsubst --strip,,$(FLAGS2)) $(GPLCFLAGS) -L -shared $^ $(FLAGS3)

sepi.lib: sepi.dll
	echo "EXPORTS" > sepi.def && nm sepi.dll | sed -n -e's/^.* T _\(.*\)$$/\1/p' >> sepi.def
	dlltool --def sepi.def --dllname sepi.dll --output-lib sepi.lib

dassault.zip: sepi.dll sepi.exe
	rm -f $@
	zip -j $@ $^ `ldd $< | sed -n -e 's/^.*=> \(\/usr\/bin\/.*\.dll\).*$$/\1/p'`

sepi.exe: sepi.c sepi.dll
	rm -f sepi.lib
	gcc -o $@ $< -L. -lsepi

BiochamGUI:	gui/Makefile
	cd gui && make BiochamGUI.exe

local:
	[ "$(prefix)" =  "/local/tools/share/biocham" ] || ./configure --prefix /local/tools/share/biocham
	make install
	-chgrp -R lifeware /local/tools/share/biocham
	-find /local/tools/share/biocham -uid $$(id -u) -not -perm +0020 | xargs chmod g+w
	-for dir in bin etc include lib man; do for file in /local/tools/share/biocham/$$dir/* ; do ln -fs $$file /local/tools/$$dir/ ; done ; done
	rsync -az /local/tools/share/biocham/ /nfs/lifeware-5To/tools/share/biocham/

all-local: $(bin_PROGRAMS)
	./$(bin_PROGRAMS) --web --dump-grammar > grammar

# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
.NOEXPORT:
