[Bio] / SubsystemExtension / Makefile Repository:
ViewVC logotype

View of /SubsystemExtension/Makefile

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.4 - (download) (annotate)
Thu May 4 04:12:24 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
CVS Tags: HEAD
Changes since 1.3: +1 -1 lines
RAE: Adding automatic subsystems extension and queue to Heikos tool

#
# Copyright (c) 2003-2006 University of Chicago and Fellowship
# for Interpretations of Genomes. All Rights Reserved.
#
# This file is part of the SEED Toolkit.
# 
# The SEED Toolkit is free software. You can redistribute
# it and/or modify it under the terms of the SEED Toolkit
# Public License. 
#
# You should have received a copy of the SEED Toolkit Public License
# along with this program; if not write to the University of Chicago
# at info@ci.uchicago.edu or the Fellowship for Interpretation of
# Genomes at veronika@thefig.info or download a copy from
# http://www.theseed.org/LICENSE.TXT.
#

PERL = $(RTROOT)/env/$(RTARCH)/bin/perl

PERL_OPEN_CGI_SRC = aeos.cgi gecko.cgi

PERL_BIN_SRC = cluster_detection.pl evaluate_gecko.pl evaluate_gecko_joining.pl \
	multiple_subsystem_extension.pl subsystem_extension.pl check_subsystem_extension.pl

PERL_OPEN_CGI = $(subst .pl,.cgi, $(PERL_OPEN_CGI_SRC))
PERL_PROTECTED_CGI = $(subst .pl,.cgi, $(PERL_PROTECTED_CGI_SRC))
PERL_BIN = $(subst .pl,, $(PERL_BIN_SRC))

INST_PERL_OPEN_CGI = $(foreach var, $(PERL_OPEN_CGI), $(cgidir)/$(var)) 
INST_PERL_PROTECTED_CGI = $(foreach var, $(PERL_PROTECTED_CGI), $(cgidir)/p2p/$(var)) 
INST_PERL_BIN = $(foreach var, $(PERL_BIN), $(bindir)/$(var))

PERL_LIB = \
	AEOS.pm \
	Cluster.pm \
	ClusterDetection.pm \
	ClusterDetectionArray.pm \
	ClusterDetectionSparse.pm \
	ClusterList.pm \
	ClusterView.pm \
	ClusterView/GFX.pm \
	ClusterView/SVG.pm \
	ExtensionConfig.pm \
	ExtensionInterface.pm \
	ExtensionInterface/GENDB.pm \
	ExtensionInterface/SEED.pm \
	GeckoConfig.pm \
	GeckoInterface.pm \
	GeckoInterface/SEED.pm \
	GeckoInterface/StandAlone.pm \
	JoinedCluster.pm \
	RoleCandidate.pm \
	RoleCandidate/GENDB.pm \
	RoleCandidate/SEED.pm \
	RoleCandidateFactory.pm \
	RoleCandidateFactory/BLAST.pm \
	RoleCandidateFactory/Fasta.pm \
	RoleCandidateFactory/GENDB.pm \
	RoleCandidateFactory/SEED.pm \
	RoleCandidateFactory/MultiSEED.pm \
	RoleCandidateMatch.pm \
	RoleCandidateScore.pm \
	RoleFamilies.pm \
	SequenceFactory.pm \
	SequenceFactory/COG.pm \
	SequenceFactory/SEED.pm \
	SubsystemCandidate.pm \
	SubsystemCandidate/GENDB.pm \
	SubsystemCandidate/SEED.pm \
	SubsystemCandidateFactory.pm \
	SubsystemCandidateFactory/GENDB.pm \
	SubsystemCandidateFactory/SEED.pm \
	SubsystemCandidateFactory/MultiSEED.pm \
	SubsystemVariant.pm \
	ValidationInterface.pm \
	VariantAnalysis.pm 


INST_PERL_LIB = $(foreach var, $(PERL_LIB), $(libdir)/$(PKGNAME)/$(var))

lib:  $(INST_PYTHON_OPEN_CGI) $(INST_PYTHON_PROTECTED_CGI) \
	$(INST_PERL_OPEN_CGI) $(INST_PERL_PROTECTED_CGI) $(INST_PERL_LIB)

bin: $(INST_PYTHON_BIN) $(INST_PERL_BIN)

force:

show:
	@echo $(PYTHON_CGI_SRC)
	@echo $(PYTHON_CGI)
	@echo $(INST_PYTHON_CGI)

schematools:
stDeclFiles:
stGeneratedFiles:


test:

clean:

#TOOL_HDR := $(workdir)/tool_hdr
#TOOL_HDR_PY := $(workdir)/tool_hdr_py

#
# seed_running_perl.fragement is the piece of perl code that
# checks to see if the seed server is up, and prints a message and returns
# if it is not.
#

SEED_RUNNING_PERL = ../FigWebServices/seed_running_perl.fragment 

$(cgidir)/%.cgi: $(TOPDIR)/$(PKGNAME)/%.py $(TOOL_HDR_PY) 
	( cat $(TOOL_HDR_PY) $< > $@; chmod +x $@ )

$(cgidir)/p2p/%.cgi: $(TOPDIR)/$(PKGNAME)/%.py $(TOOL_HDR_PY)
	( cat $(TOOL_HDR_PY) $< > $@; chmod +x $@ )

$(cgidir)/%.cgi: $(TOPDIR)/$(PKGNAME)/%.pl $(TOOL_HDR) $(SEED_RUNNING_PERL)
	( cat $(TOOL_HDR) $(SEED_RUNNING_PERL) $< > $@; chmod +x $@ )

$(cgidir)/p2p/%.cgi: $(TOPDIR)/$(PKGNAME)/%.pl $(TOOL_HDR) $(SEED_RUNNING_PERL)
	( cat $(TOOL_HDR) $(SEED_RUNNING_PERL) $< > $@; chmod +x $@ )

$(bindir)/%: $(TOPDIR)/$(PKGNAME)/%.py $(TOOL_HDR_PY)
	( cat $(TOOL_HDR_PY) $< > $@; chmod +x $@ )

$(bindir)/%: $(TOPDIR)/$(PKGNAME)/%.pl $(TOOL_HDR)
	( cat $(TOOL_HDR) $< > $@; chmod +x $@ )

#
# Since our lib files have directories, need to create the target
# directory if it doesn't yet exist.
#
$(libdir)/$(PKGNAME)/%.pm: $(TOPDIR)/$(PKGNAME)/%.pm
	tgt_dir=`dirname $@`;  \
	if [ ! -d $$tgt_dir ] ; then \
		mkdir $$tgt_dir; \
	fi
	cp -p  $< $@


MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3