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1 : paarmann 1.1 #
2 :     # Copyright (c) 2003-2006 University of Chicago and Fellowship
3 :     # for Interpretations of Genomes. All Rights Reserved.
4 :     #
5 :     # This file is part of the SEED Toolkit.
6 : parrello 1.12 #
7 : paarmann 1.1 # The SEED Toolkit is free software. You can redistribute
8 :     # it and/or modify it under the terms of the SEED Toolkit
9 : parrello 1.12 # Public License.
10 : paarmann 1.1 #
11 :     # You should have received a copy of the SEED Toolkit Public License
12 :     # along with this program; if not write to the University of Chicago
13 :     # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14 :     # Genomes at veronika@thefig.info or download a copy from
15 :     # http://www.theseed.org/LICENSE.TXT.
16 :     #
17 :    
18 :     #
19 :     # seed_running_perl.fragement is the piece of perl code that
20 :     # checks to see if the seed server is up, and prints a message and returns
21 :     # if it is not.
22 :     #
23 : parrello 1.12 SEED_RUNNING_PERL = seed_running_perl.fragment
24 : paarmann 1.1
25 :     PERLCGISCRIPTS := $(subst .pl,,$(wildcard *.cgi))
26 :    
27 : olson 1.26 PERL_LIB = $(wildcard *.pm)
28 :    
29 :     # $(wildcard WebPage/*.pm) \
30 :     # $(wildcard WebApp/*.pm) \
31 :     # $(wildcard WebApplicationServer/*.pm)
32 : paczian 1.6
33 :     WEBPAGES := $(wildcard *.tmpl)
34 :    
35 : olson 1.33 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 : olson 1.32 rp_submit_sims.pl \
39 : olson 1.7 rp_auto_assign.pl rp_quality_check.pl rp_correction.pl rp_compute_bbhs.pl \
40 : olson 1.10 find-genomes-not-in-seed rp_rapid_propagation.pl rp_glue_contigs.pl rp_compute_pchs.pl \
41 : olson 1.13 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 \
43 :     imp_merge_sims.pl imp_check_tl_sim_status.pl imp_finish_tl_sims.pl \
44 : olson 1.15 imp_salvage.pl imp_submit_tl_sims.pl \
45 : olson 1.18 rp_HMM_PFAM_search_on_timelogic.pl rp_PFAM_attribute_generation.pl rp_make_PFAM_HMM_derived_attributes.pl \
46 : mkubal 1.16 validate_tl_sims.pl \
47 : olson 1.21 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 : olson 1.23 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 : mkubal 1.28 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 : olson 1.27 get_nmpdr_group.pl reset_stage.pl rp_lustre_finish.pl rp_write_exports.pl \
57 : olson 1.29 reset-failed-rp.pl \
58 : olson 1.30 rp_compute_peer_sim_pair.pl rp_request_peer_sims.pl rp_peer_sim_status.pl \
59 : olson 1.31 show_import_list.pl \
60 : olson 1.33 check_jobs_plasmid.pl rp_rapid_propagation_plasmid.pl \
61 : olson 1.35 batch_rast.pl boot_rast_servers.pl shutdown_rast_servers.pl \
62 : olson 1.36 compute_job_signature.pl save_job_signature.pl replicate_job.pl \
63 : olson 1.37 send_job_completion_email.pl rastq.pl
64 : olson 1.18
65 : olson 1.2
66 : paarmann 1.1 INST_PERL_LIB = $(foreach var, $(PERL_LIB), $(libdir)/$(PKGNAME)/$(var))
67 : olson 1.2 PERL_BIN = $(subst .pl,, $(PERL_BIN_SRC))
68 :     INST_PERL_BIN = $(foreach var, $(PERL_BIN), $(bindir)/$(var))
69 : paarmann 1.1
70 :     all: lib
71 :    
72 :     show:
73 :     @echo cgis $(foreach var, $(PERLCGISCRIPTS), $(cgidir)/$(var))
74 :     @echo top $(TOPDIR)
75 :     @echo pkg $(PKGNAME)
76 :     @echo toolhdr $(TOOL_HDR)
77 : olson 1.2
78 :     bin: $(INST_PERL_BIN)
79 : paarmann 1.1
80 : olson 1.30 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 : paarmann 1.1
87 :     htaccess_src = $(RTROOT)/config/all.htaccess
88 :     htaccess_dst = $(cgidir)/.htaccess
89 :    
90 :     copy_htaccess: force
91 :     if test -f $(htaccess_src); then \
92 :     cp $(htaccess_src) $(htaccess_dst) ; \
93 :     fi
94 :    
95 :     force:
96 :    
97 :     schematools:
98 :     stDeclFiles:
99 :     stGeneratedFiles:
100 :    
101 :    
102 :     test:
103 :    
104 :     clean:
105 :    
106 :     $(cgidir)/%: $(TOPDIR)/$(PKGNAME)/% $(TOOL_HDR)
107 :     ( cat $(TOOL_HDR) $< > $@; chmod +x $@ )
108 : olson 1.30 ifneq (,$(findstring public_html, $(cgidir)))
109 :     chmod go-w $@
110 :     endif
111 : paarmann 1.1
112 : paczian 1.6 $(cgidir)/Html/%: $(TOPDIR)/$(PKGNAME)/%
113 : parrello 1.12 cp $< $(cgidir)/Html/.
114 : paczian 1.6
115 : paarmann 1.1 #
116 :     # We have a config problem at the moment. I do not want to depend
117 :     # upon explicit calls to other packages, as done here nor do I want
118 :     # to assume that package was built first. For now, we live with this.
119 :    
120 :     #$(TOOL_HDR):
121 :     # cd $(workdir); $(TOPDIR)/FigCommon/configure-env $(RTARCH) $(TOPDIR)
122 :    
123 :    
124 :     #
125 :     # Since our lib files have directories, need to create the target
126 :     # directory if it doesn't yet exist.
127 :     #
128 :     $(libdir)/$(PKGNAME)/%.pm: $(TOPDIR)/$(PKGNAME)/%.pm
129 :     tgt_dir=`dirname $@`; \
130 :     if [ ! -d $$tgt_dir ] ; then \
131 :     mkdir $$tgt_dir; \
132 :     fi
133 : parrello 1.12 cp $< $@
134 : paarmann 1.1
135 : olson 1.2 $(bindir)/%: $(TOPDIR)/$(PKGNAME)/%.pl $(TOOL_HDR)
136 :     ( cat $(TOOL_HDR) $< > $@; chmod +x $@ )
137 :    
138 : olson 1.17 # perl -I.. -c $<
139 :    

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