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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 1.4 PERL_BIN_SRC = check_jobs.pl rp_chunk_sims.pl rp_compute_sims.pl rp_postproc_sims.pl \
36 : olson 1.7 rp_auto_assign.pl rp_quality_check.pl rp_correction.pl rp_compute_bbhs.pl \
37 : olson 1.10 find-genomes-not-in-seed rp_rapid_propagation.pl rp_glue_contigs.pl rp_compute_pchs.pl \
38 : olson 1.13 migrate_job.pl rp_scenarios.pl \
39 :     create_import_job.pl import_pipeline.pl imp_build_nr.pl imp_prepare_sims.pl imp_process_sims.pl \
40 :     imp_merge_sims.pl imp_check_tl_sim_status.pl imp_finish_tl_sims.pl \
41 : olson 1.15 imp_salvage.pl imp_submit_tl_sims.pl \
42 : olson 1.18 rp_HMM_PFAM_search_on_timelogic.pl rp_PFAM_attribute_generation.pl rp_make_PFAM_HMM_derived_attributes.pl \
43 : mkubal 1.16 validate_tl_sims.pl \
44 : olson 1.21 rp_critica.pl rp_glimmer.pl rp_gen_teach_sims.pl rp_index_attributes.pl \
45 :     rp_HMM_PFAM_search_on_timelogic.pl rp_PFAM_attribute_generation.pl rp_make_PFAM_HMM_derived_attributes.pl \
46 : olson 1.23 rp_CELLO_attribute_generation.pl rp_CELLO_search.pl rp_make_CELLO_attributes.pl \
47 :     rp_PHOBIUS_attribute_generation.pl rp_PHOBIUS_search.pl rp_make_PHOBIUS_attributes.pl \
48 : mkubal 1.28 rp_PSORT_attribute_generation.pl rp_run_PSORT_on_genome.pl rp_make_PSORT_attributes.pl \
49 :     rp_genome_phenotype_attribute_generation.pl rp_make_genome_phenotype_attributes.pl \
50 :     rp_mw_and_pi_attribute_generation.pl rp_make_mw_and_pi_attributes.pl \
51 :     rp_similar_to_human_attribute_generation.pl rp_run_blast_against_human.pl rp_make_similar_to_human_attributes.pl \
52 :     rp_interpro_download_attribute_generation.pl rp_compute_crc64_for_pegs_in_genome.pl rp_make_interpro_download_attributes.pl \
53 : olson 1.27 get_nmpdr_group.pl reset_stage.pl rp_lustre_finish.pl rp_write_exports.pl \
54 : olson 1.29 reset-failed-rp.pl \
55 : olson 1.30 rp_compute_peer_sim_pair.pl rp_request_peer_sims.pl rp_peer_sim_status.pl \
56 :     show_import_list.pl
57 : olson 1.18
58 : olson 1.2
59 : paarmann 1.1 INST_PERL_LIB = $(foreach var, $(PERL_LIB), $(libdir)/$(PKGNAME)/$(var))
60 : olson 1.2 PERL_BIN = $(subst .pl,, $(PERL_BIN_SRC))
61 :     INST_PERL_BIN = $(foreach var, $(PERL_BIN), $(bindir)/$(var))
62 : paarmann 1.1
63 :     all: lib
64 :    
65 :     show:
66 :     @echo cgis $(foreach var, $(PERLCGISCRIPTS), $(cgidir)/$(var))
67 :     @echo top $(TOPDIR)
68 :     @echo pkg $(PKGNAME)
69 :     @echo toolhdr $(TOOL_HDR)
70 : olson 1.2
71 :     bin: $(INST_PERL_BIN)
72 : paarmann 1.1
73 : olson 1.30 lib: $(foreach var, $(PERLCGISCRIPTS), $(cgidir)/$(var)) copy_htaccess $(INST_PERL_LIB) $(foreach var, $(WEBPAGES), $(cgidir)/Html/$(var)) fix_web_perms
74 :    
75 :     fix_web_perms:
76 :     ifneq (,$(findstring public_html, $(cgidir)))
77 :     chmod go-w $(cgidir)
78 :     endif
79 : paarmann 1.1
80 :     htaccess_src = $(RTROOT)/config/all.htaccess
81 :     htaccess_dst = $(cgidir)/.htaccess
82 :    
83 :     copy_htaccess: force
84 :     if test -f $(htaccess_src); then \
85 :     cp $(htaccess_src) $(htaccess_dst) ; \
86 :     fi
87 :    
88 :     force:
89 :    
90 :     schematools:
91 :     stDeclFiles:
92 :     stGeneratedFiles:
93 :    
94 :    
95 :     test:
96 :    
97 :     clean:
98 :    
99 :     $(cgidir)/%: $(TOPDIR)/$(PKGNAME)/% $(TOOL_HDR)
100 :     ( cat $(TOOL_HDR) $< > $@; chmod +x $@ )
101 : olson 1.30 ifneq (,$(findstring public_html, $(cgidir)))
102 :     chmod go-w $@
103 :     endif
104 : paarmann 1.1
105 : paczian 1.6 $(cgidir)/Html/%: $(TOPDIR)/$(PKGNAME)/%
106 : parrello 1.12 cp $< $(cgidir)/Html/.
107 : paczian 1.6
108 : paarmann 1.1 #
109 :     # We have a config problem at the moment. I do not want to depend
110 :     # upon explicit calls to other packages, as done here nor do I want
111 :     # to assume that package was built first. For now, we live with this.
112 :    
113 :     #$(TOOL_HDR):
114 :     # cd $(workdir); $(TOPDIR)/FigCommon/configure-env $(RTARCH) $(TOPDIR)
115 :    
116 :    
117 :     #
118 :     # Since our lib files have directories, need to create the target
119 :     # directory if it doesn't yet exist.
120 :     #
121 :     $(libdir)/$(PKGNAME)/%.pm: $(TOPDIR)/$(PKGNAME)/%.pm
122 :     tgt_dir=`dirname $@`; \
123 :     if [ ! -d $$tgt_dir ] ; then \
124 :     mkdir $$tgt_dir; \
125 :     fi
126 : parrello 1.12 cp $< $@
127 : paarmann 1.1
128 : olson 1.2 $(bindir)/%: $(TOPDIR)/$(PKGNAME)/%.pl $(TOOL_HDR)
129 :     ( cat $(TOOL_HDR) $< > $@; chmod +x $@ )
130 :    
131 : olson 1.17 # perl -I.. -c $<
132 :    

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