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revision 1.15, Tue Sep 25 18:45:53 2007 UTC revision 1.37, Wed Jan 27 17:37:00 2010 UTC
# Line 24  Line 24 
24    
25  PERLCGISCRIPTS := $(subst .pl,,$(wildcard *.cgi))  PERLCGISCRIPTS := $(subst .pl,,$(wildcard *.cgi))
26    
27  PERL_LIB = $(wildcard *.pm) \  PERL_LIB = $(wildcard *.pm)
28             $(wildcard WebPage/*.pm) \  
29             $(wildcard WebApp/*.pm) \  #          $(wildcard WebPage/*.pm) \
30             $(wildcard WebApplicationServer/*.pm)  #           $(wildcard WebApp/*.pm) \
31    #           $(wildcard WebApplicationServer/*.pm)
32    
33  WEBPAGES := $(wildcard *.tmpl)  WEBPAGES := $(wildcard *.tmpl)
34    
35  PERL_BIN_SRC = check_jobs.pl rp_chunk_sims.pl rp_compute_sims.pl rp_postproc_sims.pl  \  PERL_BIN_SRC = check_jobs.pl rp_chunk_sims.pl rp_compute_sims.pl rp_postproc_sims.pl  rp_preprocess_sims.pl \
36            pull_sims_from_server.pl  \
37            pull_sims_from_database.pl  \
38            rp_submit_sims.pl \
39          rp_auto_assign.pl rp_quality_check.pl rp_correction.pl rp_compute_bbhs.pl \          rp_auto_assign.pl rp_quality_check.pl rp_correction.pl rp_compute_bbhs.pl \
40          find-genomes-not-in-seed rp_rapid_propagation.pl  rp_glue_contigs.pl  rp_compute_pchs.pl \          find-genomes-not-in-seed rp_rapid_propagation.pl  rp_glue_contigs.pl  rp_compute_pchs.pl \
41          migrate_job.pl rp_scenarios.pl \          migrate_job.pl rp_scenarios.pl \
42          create_import_job.pl import_pipeline.pl imp_build_nr.pl imp_prepare_sims.pl imp_process_sims.pl \          create_import_job.pl import_pipeline.pl imp_build_nr.pl imp_prepare_sims.pl imp_process_sims.pl \
43          imp_merge_sims.pl imp_check_tl_sim_status.pl  imp_finish_tl_sims.pl  \          imp_merge_sims.pl imp_check_tl_sim_status.pl  imp_finish_tl_sims.pl  \
44          imp_salvage.pl imp_submit_tl_sims.pl \          imp_salvage.pl imp_submit_tl_sims.pl \
45          validate_tl_sims.pl          rp_HMM_PFAM_search_on_timelogic.pl rp_PFAM_attribute_generation.pl rp_make_PFAM_HMM_derived_attributes.pl \
46            validate_tl_sims.pl \
47            rp_critica.pl rp_glimmer.pl rp_gen_teach_sims.pl rp_index_attributes.pl \
48            rp_HMM_PFAM_search_on_timelogic.pl rp_PFAM_attribute_generation.pl rp_make_PFAM_HMM_derived_attributes.pl \
49            rp_CELLO_attribute_generation.pl rp_CELLO_search.pl rp_make_CELLO_attributes.pl \
50            rp_PHOBIUS_attribute_generation.pl rp_PHOBIUS_search.pl rp_make_PHOBIUS_attributes.pl \
51            rp_PSORT_attribute_generation.pl rp_run_PSORT_on_genome.pl rp_make_PSORT_attributes.pl \
52            rp_genome_phenotype_attribute_generation.pl rp_make_genome_phenotype_attributes.pl \
53            rp_mw_and_pi_attribute_generation.pl rp_make_mw_and_pi_attributes.pl \
54            rp_similar_to_human_attribute_generation.pl rp_run_blast_against_human.pl rp_make_similar_to_human_attributes.pl \
55            rp_interpro_download_attribute_generation.pl rp_compute_crc64_for_pegs_in_genome.pl rp_make_interpro_download_attributes.pl \
56            get_nmpdr_group.pl reset_stage.pl rp_lustre_finish.pl rp_write_exports.pl \
57            reset-failed-rp.pl \
58            rp_compute_peer_sim_pair.pl rp_request_peer_sims.pl rp_peer_sim_status.pl \
59            show_import_list.pl \
60            check_jobs_plasmid.pl rp_rapid_propagation_plasmid.pl  \
61            batch_rast.pl boot_rast_servers.pl shutdown_rast_servers.pl \
62            compute_job_signature.pl save_job_signature.pl replicate_job.pl \
63            send_job_completion_email.pl rastq.pl
64    
65    
66  INST_PERL_LIB = $(foreach var, $(PERL_LIB), $(libdir)/$(PKGNAME)/$(var))  INST_PERL_LIB = $(foreach var, $(PERL_LIB), $(libdir)/$(PKGNAME)/$(var))
# Line 55  Line 77 
77    
78  bin: $(INST_PERL_BIN)  bin: $(INST_PERL_BIN)
79    
80  lib:    $(foreach var, $(PERLCGISCRIPTS), $(cgidir)/$(var)) copy_htaccess $(INST_PERL_LIB) $(foreach var, $(WEBPAGES), $(cgidir)/Html/$(var))  lib:    $(foreach var, $(PERLCGISCRIPTS), $(cgidir)/$(var)) copy_htaccess $(INST_PERL_LIB) $(foreach var, $(WEBPAGES), $(cgidir)/Html/$(var)) fix_web_perms
81    
82    fix_web_perms:
83    ifneq (,$(findstring public_html, $(cgidir)))
84            chmod go-w $(cgidir)
85    endif
86    
87  htaccess_src = $(RTROOT)/config/all.htaccess  htaccess_src = $(RTROOT)/config/all.htaccess
88  htaccess_dst = $(cgidir)/.htaccess  htaccess_dst = $(cgidir)/.htaccess
# Line 78  Line 105 
105    
106  $(cgidir)/%: $(TOPDIR)/$(PKGNAME)/% $(TOOL_HDR)  $(cgidir)/%: $(TOPDIR)/$(PKGNAME)/% $(TOOL_HDR)
107          ( cat $(TOOL_HDR) $< > $@; chmod +x $@ )          ( cat $(TOOL_HDR) $< > $@; chmod +x $@ )
108    ifneq (,$(findstring public_html, $(cgidir)))
109            chmod go-w $@
110    endif
111    
112  $(cgidir)/Html/%: $(TOPDIR)/$(PKGNAME)/%  $(cgidir)/Html/%: $(TOPDIR)/$(PKGNAME)/%
113          cp $< $(cgidir)/Html/.          cp $< $(cgidir)/Html/.
# Line 103  Line 133 
133          cp  $< $@          cp  $< $@
134    
135  $(bindir)/%: $(TOPDIR)/$(PKGNAME)/%.pl $(TOOL_HDR)  $(bindir)/%: $(TOPDIR)/$(PKGNAME)/%.pl $(TOOL_HDR)
         perl -I.. -c $<  
136          ( cat $(TOOL_HDR) $< > $@; chmod +x $@ )          ( cat $(TOOL_HDR) $< > $@; chmod +x $@ )
137    
138    #       perl -I.. -c $<
139    

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