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Revision 1.32 - (download) (annotate)
Wed Jul 8 20:18:46 2009 UTC (10 years, 5 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2009_0925, rast_rel_2009_07_09
Changes since 1.31: +2 -1 lines
Add support for pulling sims from sims server and submitting only those that don't match to be computed.

Add use of $FIG_Config::rast_sims_data to point at the directory holding
nr & peg.synonyms; explicitly here for the purposes of more easily updating
to new sims databases.

# 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.

# 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 = seed_running_perl.fragment

PERLCGISCRIPTS := $(subst .pl,,$(wildcard *.cgi))

PERL_LIB = $(wildcard *.pm) 

#	   $(wildcard WebPage/*.pm) \
#           $(wildcard WebApp/*.pm) \
#           $(wildcard WebApplicationServer/*.pm)

WEBPAGES := $(wildcard *.tmpl)

PERL_BIN_SRC = check_jobs.pl rp_chunk_sims.pl rp_compute_sims.pl rp_postproc_sims.pl  rp_preprocess_sims.pl pull_sims_from_server.pl  \
	rp_submit_sims.pl \
	rp_auto_assign.pl rp_quality_check.pl rp_correction.pl rp_compute_bbhs.pl \
	find-genomes-not-in-seed rp_rapid_propagation.pl  rp_glue_contigs.pl  rp_compute_pchs.pl \
	migrate_job.pl rp_scenarios.pl \
	create_import_job.pl import_pipeline.pl imp_build_nr.pl imp_prepare_sims.pl imp_process_sims.pl \
	imp_merge_sims.pl imp_check_tl_sim_status.pl  imp_finish_tl_sims.pl  \
	imp_salvage.pl imp_submit_tl_sims.pl \
        rp_HMM_PFAM_search_on_timelogic.pl rp_PFAM_attribute_generation.pl rp_make_PFAM_HMM_derived_attributes.pl \
	validate_tl_sims.pl \
	rp_critica.pl rp_glimmer.pl rp_gen_teach_sims.pl rp_index_attributes.pl \
	rp_HMM_PFAM_search_on_timelogic.pl rp_PFAM_attribute_generation.pl rp_make_PFAM_HMM_derived_attributes.pl \
	rp_CELLO_attribute_generation.pl rp_CELLO_search.pl rp_make_CELLO_attributes.pl \
	rp_PHOBIUS_attribute_generation.pl rp_PHOBIUS_search.pl rp_make_PHOBIUS_attributes.pl \
	rp_PSORT_attribute_generation.pl rp_run_PSORT_on_genome.pl rp_make_PSORT_attributes.pl \
	rp_genome_phenotype_attribute_generation.pl rp_make_genome_phenotype_attributes.pl \
	rp_mw_and_pi_attribute_generation.pl rp_make_mw_and_pi_attributes.pl \
	rp_similar_to_human_attribute_generation.pl rp_run_blast_against_human.pl rp_make_similar_to_human_attributes.pl \
	rp_interpro_download_attribute_generation.pl rp_compute_crc64_for_pegs_in_genome.pl rp_make_interpro_download_attributes.pl \
	get_nmpdr_group.pl reset_stage.pl rp_lustre_finish.pl rp_write_exports.pl \
	reset-failed-rp.pl \
	rp_compute_peer_sim_pair.pl rp_request_peer_sims.pl rp_peer_sim_status.pl \
	show_import_list.pl \
	check_jobs_plasmid.pl rp_rapid_propagation_plasmid.pl 

INST_PERL_LIB = $(foreach var, $(PERL_LIB), $(libdir)/$(PKGNAME)/$(var))
PERL_BIN = $(subst .pl,, $(PERL_BIN_SRC))
INST_PERL_BIN = $(foreach var, $(PERL_BIN), $(bindir)/$(var))

all: lib

	@echo cgis $(foreach var, $(PERLCGISCRIPTS), $(cgidir)/$(var))
	@echo top $(TOPDIR)
	@echo pkg $(PKGNAME)
	@echo toolhdr $(TOOL_HDR)


lib:	$(foreach var, $(PERLCGISCRIPTS), $(cgidir)/$(var)) copy_htaccess $(INST_PERL_LIB) $(foreach var, $(WEBPAGES), $(cgidir)/Html/$(var)) fix_web_perms

ifneq (,$(findstring public_html, $(cgidir)))
	chmod go-w $(cgidir)

htaccess_src = $(RTROOT)/config/all.htaccess
htaccess_dst = $(cgidir)/.htaccess

copy_htaccess: force
	if test -f $(htaccess_src); then \
		 cp $(htaccess_src) $(htaccess_dst) ; \





$(cgidir)/%: $(TOPDIR)/$(PKGNAME)/% $(TOOL_HDR)
	( cat $(TOOL_HDR) $< > $@; chmod +x $@ )
ifneq (,$(findstring public_html, $(cgidir)))
	chmod go-w $@

$(cgidir)/Html/%: $(TOPDIR)/$(PKGNAME)/%
	cp $< $(cgidir)/Html/.

# We have a config problem at the moment.  I do not want to depend
# upon explicit calls to other packages, as done here nor do I want
# to assume that package was built first.  For now, we live with this.

#	cd $(workdir); $(TOPDIR)/FigCommon/configure-env $(RTARCH) $(TOPDIR)

# 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; \
	cp  $< $@

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

#	perl -I.. -c $<

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