#-------------
# make PROGRAM=x 	: make html and cgi for program x (default: clustalw)
# make install PROGRAM=x : copy html and cgi files in the appropriate
# 			   directories HTML-INSTALL-DIR and CGI-INSTALL-DIR
# make connect		: make connections between programs (pipe attribute)
#                         and generates the PerDef/pipeins file
# make applis		: run make for each program in PROGRAMS
# make install_applis	: run make install for each program in PROGRAMS

# *** for Web configuration, see lib/web.pl ***

VERSION=5.a

# do not edit the Makefile, nor the Makefile.in
# the file to be edited is Makefile.global
include Makefile.global

# directory where you downloaded Pise
DOWNLOAD = /local/gensoft/lib/Pise
PISEDIR = $(DOWNLOAD)/5.a

# There should be nothing to changes below
#################################################################3

# directories for generated Html, Cgi, etc... files (before installation)
HTML-DIR = ./Html
CGI-DIR = ./Cgi
TCL-DIR = ./Tcl
BIOK-DIR = ./Biok
XML-DIR = ./Xml
BIOPERL-DIR = ./Bio
PYTHON-DIR = ./Python
SEQLAB-DIR = ./SeqLab
SEWER-DIR = ./SeWer
# other directories
MAKER-DIR = ./Maker
PARSER-DIR = ./Parser
DISTRIB-DIR = ./Distrib
PERLDEF-DIR = ./PerlDef

DISTRIB = ./$(VERSION)/Makefile \
	./$(VERSION)/Makefile.in \
	./$(VERSION)/Makefile.global \
	./$(VERSION)/Makefile.bioperl \
	./$(VERSION)/ChangeLog \
	./$(VERSION)/README \
	./$(VERSION)/LICENCE \
	./$(VERSION)/configure \
	./$(VERSION)/configure.in \
	./$(VERSION)/aclocal.m4 \
	./$(VERSION)/$(MAKER-DIR)/*.in \
	./$(VERSION)/$(MAKER-DIR)/*.pl \
	./$(VERSION)/$(MAKER-DIR)/*.pm \
	./$(VERSION)/$(PERLDEF-DIR)/pipeins \
	./$(VERSION)/$(PERLDEF-DIR)/*.pm \
	./$(VERSION)/$(BIOPERL-DIR) \
	./$(VERSION)/$(PYTHON-DIR)/PiseWorkflow.py \
	./$(VERSION)/$(PYTHON-DIR)/Pise/__init__.py \
	./$(VERSION)/$(SEQLAB-DIR) \
	./$(VERSION)/$(SEWER-DIR) \
	./$(VERSION)/$(PARSER-DIR)/PiseParser.pm \
	./$(VERSION)/$(PARSER-DIR)/*.in \
	./$(VERSION)/$(PARSER-DIR)/runparser.pl \
	./$(VERSION)/$(PARSER-DIR)/pise.dtd \
	./$(VERSION)/$(XML-DIR)/*.xml.in \
	./$(VERSION)/$(XML-DIR)/protdbs.xml \
	./$(VERSION)/$(XML-DIR)/nucdbs.xml \
	./$(VERSION)/$(XML-DIR)/phylip_header.xml \
	./$(VERSION)/$(XML-DIR)/glimmer_header.xml \
	./$(VERSION)/$(XML-DIR)/blast_init.xml \
	./$(VERSION)/$(XML-DIR)/fastapath.xml \
	./$(VERSION)/Examples \
	./$(VERSION)/lib/*.in \
	./$(VERSION)/lib/*.pm \
	./$(VERSION)/lib/*.pl \
	./$(VERSION)/lib/*.tcl \
	./$(VERSION)/lib/*.css \
	./$(VERSION)/lib/README \
	./$(VERSION)/Scripts \
	./$(VERSION)/Doc \
	./$(VERSION)/Images \
	./$(VERSION)/Data

DONT_DISTRIB = ./$(VERSION)/lib/check_pasteur.pl

LIGHT_DISTRIB = ./$(VERSION)/Makefile \
	./$(VERSION)/Makefile.in \
	./$(VERSION)/Makefile.global \
	./$(VERSION)/Makefile.bioperl \
	./$(VERSION)/ChangeLog \
	./$(VERSION)/README \
	./$(VERSION)/LICENCE \
	./$(VERSION)/configure \
	./$(VERSION)/configure.in \
	./$(VERSION)/aclocal.m4 \
	./$(VERSION)/$(MAKER-DIR)/*.in \
	./$(VERSION)/$(MAKER-DIR)/*.pl \
	./$(VERSION)/$(MAKER-DIR)/*.pm \
	./$(VERSION)/$(PERLDEF-DIR)/pipeins \
	./$(VERSION)/$(BIOPERL-DIR)/Factory/Pise.pm \
	./$(VERSION)/$(BIOPERL-DIR)/Tools/Run/*.pm \
	./$(VERSION)/$(BIOPERL-DIR)/Tools/Run/AnalysisFactory \
	./$(VERSION)/$(PYTHON-DIR)/PiseWorkflow.py \
	./$(VERSION)/$(PYTHON-DIR)/Pise/__init__.py \
	./$(VERSION)/$(PARSER-DIR)/PiseParser.pm \
	./$(VERSION)/$(PARSER-DIR)/*.in \
	./$(VERSION)/$(PARSER-DIR)/runparser.pl \
	./$(VERSION)/$(PARSER-DIR)/pise.dtd \
	./$(VERSION)/$(XML-DIR)/*.xml.in \
	./$(VERSION)/$(XML-DIR)/protdbs.xml \
	./$(VERSION)/$(XML-DIR)/nucdbs.xml \
	./$(VERSION)/$(XML-DIR)/phylip_header.xml \
	./$(VERSION)/$(XML-DIR)/glimmer_header.xml \
	./$(VERSION)/$(XML-DIR)/blast_init.xml \
	./$(VERSION)/$(XML-DIR)/fastapath.xml \
	./$(VERSION)/$(SEWER-DIR) \
	./$(VERSION)/Examples \
	./$(VERSION)/lib/*.in \
	./$(VERSION)/lib/*.pm \
	./$(VERSION)/lib/*.pl \
	./$(VERSION)/lib/*.tcl \
	./$(VERSION)/lib/*.css \
	./$(VERSION)/lib/README \
	./$(VERSION)/Scripts \
	./$(VERSION)/Doc \
	./$(VERSION)/Images \
	./$(VERSION)/Data

XMLDISTRIB = ./$(VERSION)/Makefile.global \
	./$(VERSION)/ChangeLog \
	./$(VERSION)/LICENCE \
	./$(VERSION)/$(XML-DIR)/*.xml.in \
	./$(VERSION)/$(XML-DIR)/protdbs.xml \
	./$(VERSION)/$(XML-DIR)/nucdbs.xml \
	./$(VERSION)/$(XML-DIR)/*_header.xml \
	./$(VERSION)/$(XML-DIR)/blast_init.xml \
	./$(VERSION)/$(XML-DIR)/fastapath.xml 

BIOPERLDISTRIB = \
	./ChangeLog \
	./LICENCE \
	./configure \
	./aclocal.m4 \
	$(BIOPERL-DIR) \
	Examples/bioperl-examples \
	./$(MAKER-DIR)/make-bioperl.pl.in

SEQLABDISTRIB = $(SEQLAB-DIR) \
	./ChangeLog \
	./LICENCE \
	./configure \
	./Makefile.in \
	./aclocal.m4 \
	./Maker/make-seqlab.pl.in

SEWERDISTRIB = $(SEWER-DIR) \
	./ChangeLog \
	./LICENCE \
	./configure \
	./Makefile.in \
	./aclocal.m4 \
	./Maker/make-sewer.pl.in

PROGRAM = clustalw

all: $(PERLDEF-DIR)/$(PROGRAM).pm $(PISEDIR)/$(HTML-DIR)/$(PROGRAM).html $(PISEDIR)/$(HTML-DIR)/$(PROGRAM)-simple.html $(PISEDIR)/$(CGI-DIR)/$(PROGRAM).pl $(TCL-DIR)/$(PROGRAM).tcl $(XML-DIR)/$(PROGRAM).xml $(BIOPERL-DIR)/Tools/Run/PiseApplication/$(PROGRAM).pm $(PYTHON-DIR)/$(PROGRAM).py

install: $(HTML-INSTALL-DIR)/$(PROGRAM)-simple.html $(HTML-INSTALL-DIR)/$(PROGRAM).html $(CGI-INSTALL-DIR)/$(PROGRAM).pl $(TCL-DIR)/$(PROGRAM).tcl $(BIOPERL-DIR)/Tools/Run/PiseApplication/$(PROGRAM).pm $(PYTHON-DIR)/$(PROGRAM).py
	@if [ ! -d $(CGI-INSTALL-DIR)/lib ]; then \
		mkdir $(CGI-INSTALL-DIR)/lib ; \
		ln -s -f $(PISEDIR)/lib/annot.pl $(CGI-INSTALL-DIR)/lib ; \
		ln -s -f $(PISEDIR)/lib/connect.pl $(CGI-INSTALL-DIR)/lib ; \
		ln -s -f $(PISEDIR)/lib/get_tcl.pl $(CGI-INSTALL-DIR)/lib ; \
		ln -s -f $(PISEDIR)/lib/help.pl $(CGI-INSTALL-DIR)/lib ; \
		ln -s -f $(PISEDIR)/lib/initform.pl $(CGI-INSTALL-DIR)/lib ; \
		ln -s -f $(PISEDIR)/lib/lsf.pl $(CGI-INSTALL-DIR)/lib ; \
		ln -s -f $(PISEDIR)/lib/mailhelp.pl $(CGI-INSTALL-DIR)/lib ; \
		ln -s -f $(PISEDIR)/lib/results.pl $(CGI-INSTALL-DIR)/lib ; \
		ln -s -f $(PISEDIR)/lib/save.pl $(CGI-INSTALL-DIR)/lib ; \
		ln -s -f $(PISEDIR)/lib/summary.pl $(CGI-INSTALL-DIR)/lib ; \
		ln -s -f $(PISEDIR)/lib/tcl.pl $(CGI-INSTALL-DIR)/lib ; \
		ln -s -f $(PISEDIR)/lib/webmacro.pl $(CGI-INSTALL-DIR)/lib ; \
		chmod -f a+rx $(PISEDIR)/lib/*.pl ; \
	fi
	@if [ ! -d $(CGI-INSTALL-DIR)/macros ]; then \
		echo "Warning: you may have to create a $(CGI-INSTALL-DIR)/macros directory writeable by the Web server" ; \
	fi

install_applis:
	for program in $(PROGRAMS) ; do \
		make install PROGRAM=$$program ; \
	done
	make connect

connect:
	@PISEDIR=$(PISEDIR); export PISEDIR ; \
		perl $(MAKER-DIR)/make-connections.pl $(PROGRAMS) $(EMBOSS) 
	@if [ ! -d $(CGI-INSTALL-DIR)/lib ]; then \
		mkdir $(CGI-INSTALL-DIR)/lib ; \
	fi

applis:
	for program in $(PROGRAMS) ; do \
		make PROGRAM=$$program all ; \
	done

emboss: $(XML-DIR)/emboss.xml
	for program in $(EMBOSS) ; do \
		make PROGRAM=$$program OPT_EMAIL=$(EMBOSS_OPT_EMAIL) all ; \
	done

install_emboss: $(XML-DIR)/emboss.xml
	for program in $(EMBOSS) ; do \
		make install PROGRAM=$$program OPT_EMAIL=$(EMBOSS_OPT_EMAIL) all ; \
	done

$(XML-DIR)/emboss.xml:  $(PISEDIR)/$(XML-DIR)/emboss.xml.in
	sed 's#PARSER#$(PISEDIR)/Parser#' $(PISEDIR)/$(XML-DIR)/emboss.xml.in | sed 's#XMLDIR#$(PISEDIR)/Xml#' | sed 's#EMBOSSDIR#$(EMBOSSDIR)#' > $@
	chmod -f g+rw $@

index: $(HTML-INSTALL-DIR)/pise.html $(HTML-INSTALL-DIR)/navframe.html $(HTML-INSTALL-DIR)/alpha.html $(HTML-INSTALL-DIR)/category.html

$(HTML-INSTALL-DIR)/pise.html: $(MAKER-DIR)/make-index.pl lib/web.pl
	PISEDIR=$(PISEDIR); export PISEDIR ; \
	VERSION=$(VERSION); export VERSION ; \
	perl $(MAKER-DIR)/make-index.pl --index=$@ --modules="$(PROGRAMS) $(EMBOSS)" >$@; \

$(HTML-INSTALL-DIR)/navframe.html: $(MAKER-DIR)/make-index.pl lib/web.pl
	PERLDEFDIR=$(PERLDEF-DIR); export PERLDEFDIR ; \
	PISEDIR=$(PISEDIR); export PISEDIR ; \
	VERSION=$(VERSION); export VERSION ; \
	perl $(MAKER-DIR)/make-index.pl --navframe=$@ --modules="$(PROGRAMS) $(EMBOSS)" >$@; \

$(HTML-INSTALL-DIR)/alpha.html: $(MAKER-DIR)/make-index.pl lib/web.pl
	PERLDEFDIR=$(PERLDEF-DIR); export PERLDEFDIR ; \
	PISEDIR=$(PISEDIR); export PISEDIR ; \
	VERSION=$(VERSION); export VERSION ; \
	perl $(MAKER-DIR)/make-index.pl --alpha=$@  --modules="$(PROGRAMS) $(EMBOSS)" >$@; \

$(HTML-INSTALL-DIR)/category.html: $(MAKER-DIR)/make-index.pl lib/web.pl
	PERLDEFDIR=$(PERLDEF-DIR); export PERLDEFDIR ; \
	PISEDIR=$(PISEDIR); export PISEDIR ; \
	VERSION=$(VERSION); export VERSION ; \
	perl $(MAKER-DIR)/make-index.pl --category=$@  --modules="$(PROGRAMS) $(EMBOSS)" >$@; \


./Cgi/$(PROGRAM).pl: $(PISEDIR)/$(CGI-DIR)/$(PROGRAM).pl
./Html/$(PROGRAM).html: $(PISEDIR)/$(HTML-DIR)/$(PROGRAM).html
./Html/$(PROGRAM)-simple.html: $(PISEDIR)/$(HTML-DIR)/$(PROGRAM)-simple.html

seqlab: $(SEQLAB-DIR)/$(PROGRAM).config

bioperl-all:
	for program in $(EMBOSS) ; do \
		make bioperl PROGRAM=$$program ; \
	done
	for program in $(BIOPERL_PROGRAMS) ; do \
		make bioperl PROGRAM=$$program ; \
	done

bioperl: $(BIOPERL-DIR)/Tools/Run/PiseApplication/$(PROGRAM).pm

#---------------------------------------------------
# Perl data structures
#

$(PERLDEF-DIR)/$(PROGRAM).pm: $(XML-DIR)/$(PROGRAM).xml $(PARSER-DIR)/runparser.pl $(PARSER-DIR)/PiseParser.pm $(MAKER-DIR)/perloo.pm
	@if [ ! -d $(PISEDIR)/$(PERLDEF-DIR) ]; then \
		mkdir $(PISEDIR)/$(PERLDEF-DIR) ; \
	fi
	PISEDIR=$(PISEDIR); export PISEDIR ; \
	VERSION=$(VERSION); export VERSION ; \
	OPT_EMAIL=$(OPT_EMAIL); export OPT_EMAIL; \
		 /local/bin/rxp -V $(XML-DIR)/$(PROGRAM).xml | $(PARSER-DIR)/runparser.pl > $@
	chmod -f g+rw $@
	chmod -f a+r $@

#---------------------------------------------------
# Xml files
#

$(XML-DIR)/$(PROGRAM).xml:  $(XML-DIR)/$(PROGRAM).xml.in
	sed 's#PARSER#$(PISEDIR)/Parser#' $(PISEDIR)/$(XML-DIR)/$(PROGRAM).xml.in | sed 's#XMLDIR#$(PISEDIR)/Xml#' > $@
	chmod -f g+rw $@

# to be used the first time you make the interface for PROGRAM
# .xml.in files are for configuration purposes
$(XML-DIR)/$(PROGRAM).xml.in:
	@if [ ! -f $(XML-DIR)/$(PROGRAM).xml.in ]; then \
		sed 's#$(PISEDIR)/Parser#PARSER#' $(PISEDIR)/$(XML-DIR)/$(PROGRAM).xml | sed 's#$(PISEDIR)/Xml#XMLDIR#' | sed 's#$(EMBOSSDIR)#EMBOSSDIR#' > $(PISEDIR)/$(XML-DIR)/$(PROGRAM).xml.in ; \
		chmod -f g+rw $(XML-DIR)/$(PROGRAM).xml.in ; \
	fi

#---------------------------------------------------
# Web part / HTML
#	- simple form
#	- advanced form

#------------------
# advanced version
#

$(PISEDIR)/$(HTML-DIR)/$(PROGRAM).html: $(PERLDEF-DIR)/$(PROGRAM).pm $(MAKER-DIR)/make-html.pl $(MAKER-DIR)/make-html-utils.pl lib/web.pl
	@if [ ! -d $(PISEDIR)/$(HTML-DIR) ]; then \
		mkdir $(PISEDIR)/$(HTML-DIR) ; \
	fi
	@VERSION=$(VERSION); export VERSION ; \
	PISEDIR=$(PISEDIR); export PISEDIR ; \
		perl $(MAKER-DIR)/make-html.pl $(PROGRAM) > $@
	chmod -f g+rw $@

#------------------
# simple version
#

$(PISEDIR)/$(HTML-DIR)/$(PROGRAM)-simple.html: $(PERLDEF-DIR)/$(PROGRAM).pm $(MAKER-DIR)/make-simple-html.pl $(MAKER-DIR)/make-html-utils.pl lib/web.pl
	@if [ ! -d $(PISEDIR)/$(HTML-DIR) ]; then \
		mkdir $(PISEDIR)/$(HTML-DIR) ; \
	fi
	@VERSION=$(VERSION); export VERSION ; \
	PISEDIR=$(PISEDIR); export PISEDIR ; \
		perl $(MAKER-DIR)/make-simple-html.pl $(PROGRAM) > $@
	chmod -f g+rw $@

$(PISEDIR)/$(CGI-DIR)/$(PROGRAM).pl: $(PERLDEF-DIR)/$(PROGRAM).pm $(MAKER-DIR)/make-cgi.pl lib/web.pl
	@if [ ! -d $(PISEDIR)/$(CGI-DIR) ]; then \
		mkdir $(PISEDIR)/$(CGI-DIR) ; \
	fi
	@VERSION=$(VERSION); export VERSION ; \
	PISEDIR=$(PISEDIR); export PISEDIR ; \
		perl $(MAKER-DIR)/make-cgi.pl $(PROGRAM) > $@
	chmod -f g+rw $@


$(TCL-DIR)/$(PROGRAM).tcl: $(PERLDEF-DIR)/$(PROGRAM).pm $(MAKER-DIR)/make-tcl.pl $(MAKER-DIR)/make-tcl-utils.pl lib/web.pl
	@if [ ! -d $(PISEDIR)/$(TCL-DIR) ]; then \
		mkdir $(PISEDIR)/$(TCL-DIR) ; \
	fi
	@VERSION=$(VERSION); export VERSION ; \
	PISEDIR=$(PISEDIR); export PISEDIR ; \
		perl $(MAKER-DIR)/make-tcl.pl $(PROGRAM) > $@
	chmod -f g+rw $@

$(BIOK-DIR)/$(PROGRAM).tcl: $(PERLDEF-DIR)/$(PROGRAM).pm $(MAKER-DIR)/make-biok.pl lib/web.pl
	@if [ ! -d $(PISEDIR)/$(BIOK-DIR) ]; then \
		mkdir $(PISEDIR)/$(BIOK-DIR) ; \
	fi
	@VERSION=$(VERSION); export VERSION ; \
	PISEDIR=$(PISEDIR); export PISEDIR ; \
		perl $(MAKER-DIR)/make-biok.pl $(PROGRAM) > $@
	chmod -f g+rw $@

$(BIOPERL-DIR)/Pise/$(PROGRAM).pm: $(PERLDEF-DIR)/$(PROGRAM).pm $(MAKER-DIR)/make-bioperl.pl lib/web.pl
	@if [ ! -d $(PISEDIR)/$(BIOPERL-DIR) ]; then \
		mkdir $(PISEDIR)/$(BIOPERL-DIR) ; \
	fi
	@if [ ! -d $(PISEDIR)/$(BIOPERL-DIR)/Pise ]; then \
		mkdir $(PISEDIR)/$(BIOPERL-DIR)/Pise ; \
	fi
	@VERSION=$(VERSION); export VERSION ; \
	PISEDIR=$(PISEDIR); export PISEDIR ; \
		perl $(MAKER-DIR)/make-bioperl.pl $(PROGRAM) > $@
	chmod -f g+rw $@

$(BIOPERL-DIR)/Tools/Run/PiseApplication/$(PROGRAM).pm: $(PERLDEF-DIR)/$(PROGRAM).pm $(MAKER-DIR)/make-bioperl.pl lib/web.pl
	@if [ ! -d $(PISEDIR)/$(BIOPERL-DIR) ]; then \
		mkdir $(PISEDIR)/$(BIOPERL-DIR) ; \
	fi
	@if [ ! -d $(PISEDIR)/$(BIOPERL-DIR)/Tools ]; then \
		mkdir $(PISEDIR)/$(BIOPERL-DIR)/Tools ; \
	fi
	@if [ ! -d $(PISEDIR)/$(BIOPERL-DIR)/Tools/Run ]; then \
		mkdir $(PISEDIR)/$(BIOPERL-DIR)/Tools/Run ; \
	fi
	@if [ ! -d $(PISEDIR)/$(BIOPERL-DIR)/Tools/Run/PiseApplication ]; then \
		mkdir $(PISEDIR)/$(BIOPERL-DIR)/Tools/Run/PiseApplication ; \
	fi
	@VERSION=$(VERSION); export VERSION ; \
	PISEDIR=$(PISEDIR); export PISEDIR ; \
		perl $(MAKER-DIR)/make-bioperl.pl $(PROGRAM) > $@
	chmod -f g+rw $@

$(PYTHON-DIR)/$(PROGRAM).py: $(PERLDEF-DIR)/$(PROGRAM).pm $(MAKER-DIR)/make-python.pl lib/web.pl
	@VERSION=$(VERSION); export VERSION ; \
	PISEDIR=$(PISEDIR); export PISEDIR ; \
		perl $(MAKER-DIR)/make-python.pl $(PROGRAM) > $@
	chmod -f g+rw $@

$(SEQLAB-DIR)/$(PROGRAM).config: $(PERLDEF-DIR)/$(PROGRAM).pm $(MAKER-DIR)/make-seqlab.pl
	@if [ ! -d $(PISEDIR)/$(SEQLAB-DIR) ]; then \
		mkdir $(PISEDIR)/$(SEQLAB-DIR) ; \
	fi
	@VERSION=$(VERSION); export VERSION ; \
	PISEDIR=$(PISEDIR); export PISEDIR ; \
		perl $(MAKER-DIR)/make-seqlab.pl $(PROGRAM) > $@
	chmod -f g+rw $@

sewerprog: 
	@if [ ! -d $(PISEDIR)/$(SEWER-DIR) ]; then \
		mkdir $(PISEDIR)/$(SEWER-DIR) ; \
	fi
	@VERSION=$(VERSION); export VERSION ; \
	PISEDIR=$(PISEDIR); export PISEDIR ; \
		perl $(MAKER-DIR)/make-sewer.pl -p $(PROGRAM) -f $(SEWER_FILE) $(TITLE) > $(SEWER_FILE).new 
	chmod -f g+rw $(SEWER_FILE).new

sewercat:
	@VERSION=$(VERSION); export VERSION ; \
	PISEDIR=$(PISEDIR); export PISEDIR ; \
		perl $(MAKER-DIR)/make-sewer.pl -c $(CATEGORY) -f $(SEWER_FILE) > $(SEWER_FILE).new 
	chmod -f g+rw $(SEWER_FILE).new ; 


$(HTML-INSTALL-DIR)/$(PROGRAM)-simple.html:	$(PISEDIR)/$(HTML-DIR)/$(PROGRAM)-simple.html
	if [ ! -d $(HTML-INSTALL-DIR) ]; then \
		mkdir $(HTML-INSTALL-DIR) ; \
	fi
	if [ -f $(HTML-INSTALL-DIR)/$(PROGRAM)-simple.html ]; then \
		cp $(PISEDIR)/$(HTML-DIR)/$(PROGRAM)-simple.html $(HTML-INSTALL-DIR)/$(PROGRAM)-simple.html; \
	else \
		cp $(PISEDIR)/$(HTML-DIR)/$(PROGRAM)-simple.html $(HTML-INSTALL-DIR)/$(PROGRAM)-simple.html; \
		chmod -f a+r $(HTML-INSTALL-DIR)/$(PROGRAM)-simple.html; \
		chmod -f g+w $(HTML-INSTALL-DIR)/$(PROGRAM)-simple.html; \
	fi

$(HTML-INSTALL-DIR)/$(PROGRAM).html:	$(PISEDIR)/$(HTML-DIR)/$(PROGRAM).html
	if [ ! -d $(HTML-INSTALL-DIR) ]; then \
		mkdir $(HTML-INSTALL-DIR) ; \
	fi
	if [ -f $(HTML-INSTALL-DIR)/$(PROGRAM).html ]; then \
		cp $(PISEDIR)/$(HTML-DIR)/$(PROGRAM).html $(HTML-INSTALL-DIR)/$(PROGRAM).html; \
	else \
		cp $(PISEDIR)/$(HTML-DIR)/$(PROGRAM).html $(HTML-INSTALL-DIR)/$(PROGRAM).html; \
		chmod -f a+r $(HTML-INSTALL-DIR)/$(PROGRAM).html; \
		chmod -f g+w $(HTML-INSTALL-DIR)/$(PROGRAM).html; \
	fi

$(CGI-INSTALL-DIR)/$(PROGRAM).pl:	$(PISEDIR)/$(CGI-DIR)/$(PROGRAM).pl
	if [ ! -d $(CGI-INSTALL-DIR) ]; then \
		mkdir $(CGI-INSTALL-DIR) ; \
	fi
	if [ -f $(CGI-INSTALL-DIR)/$(PROGRAM).pl ]; then \
		cp $(PISEDIR)/$(CGI-DIR)/$(PROGRAM).pl $(CGI-INSTALL-DIR)/$(PROGRAM).pl; \
	else \
		cp $(PISEDIR)/$(CGI-DIR)/$(PROGRAM).pl $(CGI-INSTALL-DIR)/$(PROGRAM).pl; \
		chmod -f a+rx $(CGI-INSTALL-DIR)/$(PROGRAM).pl; \
		chmod -f g+w $(CGI-INSTALL-DIR)/$(PROGRAM).pl; \
	fi


$(PARSER-DIR)/y.tab.pl: $(PARSER-DIR)/parser.y
	cd $(PARSER-DIR); byacc -P -v parser.y

distrib:
	if [ ! -d $(DISTRIB-DIR) ]; then \
		mkdir $(DISTRIB-DIR) ; \
	fi
	for p in $(PISEDIR)/$(XML-DIR)/*.xml; do \
		x=`basename $$p` ; \
		echo "x=$$x $(PISEDIR)/$(XML-DIR)/$$x.in" ; \
		sed 's#$(PISEDIR)/Parser#PARSER#' $(PISEDIR)/$(XML-DIR)/$$x | sed 's#$(PISEDIR)/Xml#XMLDIR#' | sed 's#$(EMBOSSDIR)#EMBOSSDIR#' > $(PISEDIR)/$(XML-DIR)/$$x.in ; \
	done
	cd .. ; tar cvf $(DISTRIB-DIR)/Pise-$(VERSION).tar $(DISTRIB); gzip $(DISTRIB-DIR)/Pise-$(VERSION).tar
	echo tar done


light-distrib:
	if [ ! -d $(DISTRIB-DIR) ]; then \
		mkdir $(DISTRIB-DIR) ; \
	fi
	for p in $(PISEDIR)/$(XML-DIR)/*.xml; do \
		x=`basename $$p` ; \
		echo "x=$$x $(PISEDIR)/$(XML-DIR)/$$x.in" ; \
		sed 's#$(PISEDIR)/Parser#PARSER#' $(PISEDIR)/$(XML-DIR)/$$x | sed 's#$(PISEDIR)/Xml#XMLDIR#' | sed 's#$(EMBOSSDIR)#EMBOSSDIR#' > $(PISEDIR)/$(XML-DIR)/$$x.in ; \
	done
	cd .. ; tar cvf $(DISTRIB-DIR)/Pise-light-$(VERSION).tar $(LIGHT_DISTRIB); gzip $(DISTRIB-DIR)/Pise-light-$(VERSION).tar
	echo tar done

xmldistrib:
	if [ ! -d $(DISTRIB-DIR) ]; then \
		mkdir $(DISTRIB-DIR) ; \
	fi
	for p in $(PISEDIR)/$(XML-DIR)/*.xml; do \
		x=`basename $$p` ; \
		echo "x=$$x $(PISEDIR)/$(XML-DIR)/$$x.in" ; \
		sed 's#$(PISEDIR)/Parser#PARSER#' $(PISEDIR)/$(XML-DIR)/$$x | sed 's#$(PISEDIR)/Xml#XMLDIR#' | sed 's#$(EMBOSSDIR)#EMBOSSDIR#' > $(PISEDIR)/$(XML-DIR)/$$x.in ; \
	done
	cd .. ; tar cvf $(DISTRIB-DIR)/Pise-$(VERSION)-xml.tar $(XMLDISTRIB); tar --delete $(DONT_DISTRIB) -f $(DISTRIB-DIR)/Pise-$(VERSION).tar ;gzip $(DISTRIB-DIR)/Pise-$(VERSION)-xml.tar
	echo tar done

bioperldistrib:
	if [ ! -d $(DISTRIB-DIR) ]; then \
		mkdir $(DISTRIB-DIR) ; \
	fi
	if [ -d $(DISTRIB-DIR)/pise-bioperl ]; then \
		rm -rf $(DISTRIB-DIR)/pise-bioperl ; \
	fi
	mkdir $(DISTRIB-DIR)/pise-bioperl 
	cp -r $(BIOPERLDISTRIB) $(DISTRIB-DIR)/pise-bioperl
	cd $(DISTRIB-DIR); tar cvf Bioperl-$(VERSION).tar pise-bioperl;  gzip Bioperl-$(VERSION).tar ; mv Bioperl-$(VERSION).tar.gz ../../Distrib
	echo tar done

pythondistrib:
	if [ ! -d $(DISTRIB-DIR) ]; then \
		mkdir $(DISTRIB-DIR) ; \
	fi
	if [ -d $(DISTRIB-DIR)/pise-python ]; then \
		rm -rf $(DISTRIB-DIR)/pise-python ; \
	fi
	mkdir $(DISTRIB-DIR)/pise-python
	cp -r $(PYTHON-DIR) $(DISTRIB-DIR)/pise-python
	cp -r Examples/python-examples Python/PiseWorkflow.py $(DISTRIB-DIR)/pise-python
	rm -rf $(DISTRIB-DIR)/pise-python/Pise/*.pyc
	cd $(DISTRIB-DIR)/pise-python; tar cvf Pise-python-$(VERSION).tar Pise PiseWorkflow.py python-examples;  gzip Pise-python-$(VERSION).tar ; cd ../..; mv $(DISTRIB-DIR)/pise-python/Pise-python-$(VERSION).tar.gz ../Distrib
	echo tar done

pythonexa:
	if [ ! -d $(DISTRIB-DIR) ]; then \
		mkdir $(DISTRIB-DIR) ; \
	fi
	if [ -d $(DISTRIB-DIR)/pise-python ]; then \
		rm -rf $(DISTRIB-DIR)/pise-python ; \
	fi
	mkdir $(DISTRIB-DIR)/pise-python
	cp -r Examples/python-examples $(DISTRIB-DIR)/pise-python
	cd $(DISTRIB-DIR)/pise-python; tar cvf python-examples.tar python-examples;  gzip python-examples.tar ; cd ../..; mv $(DISTRIB-DIR)/pise-python/python-examples.tar.gz ../Distrib

seqlabdistrib:
	if [ ! -d $(DISTRIB-DIR) ]; then \
		mkdir $(DISTRIB-DIR) ; \
	fi
	tar cvf $(DISTRIB-DIR)/PiseSeqLab-$(VERSION).tar $(SEQLABDISTRIB); gzip $(DISTRIB-DIR)/PiseSeqLab-$(VERSION).tar ;  mv $(DISTRIB-DIR)/PiseSeqLab-$(VERSION).tar.gz ../Distrib
	echo tar done

sewerdistrib:
	if [ ! -d $(DISTRIB-DIR) ]; then \
		mkdir $(DISTRIB-DIR) ; \
	fi
	tar cvf $(DISTRIB-DIR)/PiseSeWer-$(VERSION).tar $(SEWERDISTRIB); gzip $(DISTRIB-DIR)/PiseSeWer-$(VERSION).tar ;  mv $(DISTRIB-DIR)/PiseSeWer-$(VERSION).tar.gz ../Distrib
	echo tar done

