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Revision 1.33 - (view) (download)
| 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 : | batch_rast.pl | ||
| 62 : | olson | 1.18 | |
| 63 : | olson | 1.2 | |
| 64 : | paarmann | 1.1 | INST_PERL_LIB = $(foreach var, $(PERL_LIB), $(libdir)/$(PKGNAME)/$(var)) |
| 65 : | olson | 1.2 | PERL_BIN = $(subst .pl,, $(PERL_BIN_SRC)) |
| 66 : | INST_PERL_BIN = $(foreach var, $(PERL_BIN), $(bindir)/$(var)) | ||
| 67 : | paarmann | 1.1 | |
| 68 : | all: lib | ||
| 69 : | |||
| 70 : | show: | ||
| 71 : | @echo cgis $(foreach var, $(PERLCGISCRIPTS), $(cgidir)/$(var)) | ||
| 72 : | @echo top $(TOPDIR) | ||
| 73 : | @echo pkg $(PKGNAME) | ||
| 74 : | @echo toolhdr $(TOOL_HDR) | ||
| 75 : | olson | 1.2 | |
| 76 : | bin: $(INST_PERL_BIN) | ||
| 77 : | paarmann | 1.1 | |
| 78 : | olson | 1.30 | lib: $(foreach var, $(PERLCGISCRIPTS), $(cgidir)/$(var)) copy_htaccess $(INST_PERL_LIB) $(foreach var, $(WEBPAGES), $(cgidir)/Html/$(var)) fix_web_perms |
| 79 : | |||
| 80 : | fix_web_perms: | ||
| 81 : | ifneq (,$(findstring public_html, $(cgidir))) | ||
| 82 : | chmod go-w $(cgidir) | ||
| 83 : | endif | ||
| 84 : | paarmann | 1.1 | |
| 85 : | htaccess_src = $(RTROOT)/config/all.htaccess | ||
| 86 : | htaccess_dst = $(cgidir)/.htaccess | ||
| 87 : | |||
| 88 : | copy_htaccess: force | ||
| 89 : | if test -f $(htaccess_src); then \ | ||
| 90 : | cp $(htaccess_src) $(htaccess_dst) ; \ | ||
| 91 : | fi | ||
| 92 : | |||
| 93 : | force: | ||
| 94 : | |||
| 95 : | schematools: | ||
| 96 : | stDeclFiles: | ||
| 97 : | stGeneratedFiles: | ||
| 98 : | |||
| 99 : | |||
| 100 : | test: | ||
| 101 : | |||
| 102 : | clean: | ||
| 103 : | |||
| 104 : | $(cgidir)/%: $(TOPDIR)/$(PKGNAME)/% $(TOOL_HDR) | ||
| 105 : | ( cat $(TOOL_HDR) $< > $@; chmod +x $@ ) | ||
| 106 : | olson | 1.30 | ifneq (,$(findstring public_html, $(cgidir))) |
| 107 : | chmod go-w $@ | ||
| 108 : | endif | ||
| 109 : | paarmann | 1.1 | |
| 110 : | paczian | 1.6 | $(cgidir)/Html/%: $(TOPDIR)/$(PKGNAME)/% |
| 111 : | parrello | 1.12 | cp $< $(cgidir)/Html/. |
| 112 : | paczian | 1.6 | |
| 113 : | paarmann | 1.1 | # |
| 114 : | # We have a config problem at the moment. I do not want to depend | ||
| 115 : | # upon explicit calls to other packages, as done here nor do I want | ||
| 116 : | # to assume that package was built first. For now, we live with this. | ||
| 117 : | |||
| 118 : | #$(TOOL_HDR): | ||
| 119 : | # cd $(workdir); $(TOPDIR)/FigCommon/configure-env $(RTARCH) $(TOPDIR) | ||
| 120 : | |||
| 121 : | |||
| 122 : | # | ||
| 123 : | # Since our lib files have directories, need to create the target | ||
| 124 : | # directory if it doesn't yet exist. | ||
| 125 : | # | ||
| 126 : | $(libdir)/$(PKGNAME)/%.pm: $(TOPDIR)/$(PKGNAME)/%.pm | ||
| 127 : | tgt_dir=`dirname $@`; \ | ||
| 128 : | if [ ! -d $$tgt_dir ] ; then \ | ||
| 129 : | mkdir $$tgt_dir; \ | ||
| 130 : | fi | ||
| 131 : | parrello | 1.12 | cp $< $@ |
| 132 : | paarmann | 1.1 | |
| 133 : | olson | 1.2 | $(bindir)/%: $(TOPDIR)/$(PKGNAME)/%.pl $(TOOL_HDR) |
| 134 : | ( cat $(TOOL_HDR) $< > $@; chmod +x $@ ) | ||
| 135 : | |||
| 136 : | olson | 1.17 | # perl -I.. -c $< |
| 137 : |
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