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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 : paczian 1.6 PERL_LIB = $(wildcard *.pm) \
28 : paarmann 1.9 $(wildcard WebPage/*.pm) \
29 :     $(wildcard WebApp/*.pm) \
30 :     $(wildcard WebApplicationServer/*.pm)
31 : paczian 1.6
32 :     WEBPAGES := $(wildcard *.tmpl)
33 :    
34 : olson 1.4 PERL_BIN_SRC = check_jobs.pl rp_chunk_sims.pl rp_compute_sims.pl rp_postproc_sims.pl \
35 : olson 1.7 rp_auto_assign.pl rp_quality_check.pl rp_correction.pl rp_compute_bbhs.pl \
36 : olson 1.10 find-genomes-not-in-seed rp_rapid_propagation.pl rp_glue_contigs.pl rp_compute_pchs.pl \
37 : olson 1.13 migrate_job.pl rp_scenarios.pl \
38 :     create_import_job.pl import_pipeline.pl imp_build_nr.pl imp_prepare_sims.pl imp_process_sims.pl \
39 :     imp_merge_sims.pl imp_check_tl_sim_status.pl imp_finish_tl_sims.pl \
40 : olson 1.15 imp_salvage.pl imp_submit_tl_sims.pl \
41 : olson 1.14 validate_tl_sims.pl
42 : olson 1.13
43 : olson 1.2
44 : paarmann 1.1 INST_PERL_LIB = $(foreach var, $(PERL_LIB), $(libdir)/$(PKGNAME)/$(var))
45 : olson 1.2 PERL_BIN = $(subst .pl,, $(PERL_BIN_SRC))
46 :     INST_PERL_BIN = $(foreach var, $(PERL_BIN), $(bindir)/$(var))
47 : paarmann 1.1
48 :     all: lib
49 :    
50 :     show:
51 :     @echo cgis $(foreach var, $(PERLCGISCRIPTS), $(cgidir)/$(var))
52 :     @echo top $(TOPDIR)
53 :     @echo pkg $(PKGNAME)
54 :     @echo toolhdr $(TOOL_HDR)
55 : olson 1.2
56 :     bin: $(INST_PERL_BIN)
57 : paarmann 1.1
58 : paczian 1.6 lib: $(foreach var, $(PERLCGISCRIPTS), $(cgidir)/$(var)) copy_htaccess $(INST_PERL_LIB) $(foreach var, $(WEBPAGES), $(cgidir)/Html/$(var))
59 : paarmann 1.1
60 :     htaccess_src = $(RTROOT)/config/all.htaccess
61 :     htaccess_dst = $(cgidir)/.htaccess
62 :    
63 :     copy_htaccess: force
64 :     if test -f $(htaccess_src); then \
65 :     cp $(htaccess_src) $(htaccess_dst) ; \
66 :     fi
67 :    
68 :     force:
69 :    
70 :     schematools:
71 :     stDeclFiles:
72 :     stGeneratedFiles:
73 :    
74 :    
75 :     test:
76 :    
77 :     clean:
78 :    
79 :     $(cgidir)/%: $(TOPDIR)/$(PKGNAME)/% $(TOOL_HDR)
80 :     ( cat $(TOOL_HDR) $< > $@; chmod +x $@ )
81 :    
82 : paczian 1.6 $(cgidir)/Html/%: $(TOPDIR)/$(PKGNAME)/%
83 : parrello 1.12 cp $< $(cgidir)/Html/.
84 : paczian 1.6
85 : paarmann 1.1 #
86 :     # We have a config problem at the moment. I do not want to depend
87 :     # upon explicit calls to other packages, as done here nor do I want
88 :     # to assume that package was built first. For now, we live with this.
89 :    
90 :     #$(TOOL_HDR):
91 :     # cd $(workdir); $(TOPDIR)/FigCommon/configure-env $(RTARCH) $(TOPDIR)
92 :    
93 :    
94 :     #
95 :     # Since our lib files have directories, need to create the target
96 :     # directory if it doesn't yet exist.
97 :     #
98 :     $(libdir)/$(PKGNAME)/%.pm: $(TOPDIR)/$(PKGNAME)/%.pm
99 :     tgt_dir=`dirname $@`; \
100 :     if [ ! -d $$tgt_dir ] ; then \
101 :     mkdir $$tgt_dir; \
102 :     fi
103 : parrello 1.12 cp $< $@
104 : paarmann 1.1
105 : olson 1.2 $(bindir)/%: $(TOPDIR)/$(PKGNAME)/%.pl $(TOOL_HDR)
106 : olson 1.13 perl -I.. -c $<
107 : olson 1.2 ( cat $(TOOL_HDR) $< > $@; chmod +x $@ )
108 :    

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