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Revision 1.31 - (view) (download)

1 : efrank 1.1 #
2 : olson 1.18 # 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 :     #
7 :     # The SEED Toolkit is free software. You can redistribute
8 :     # it and/or modify it under the terms of the SEED Toolkit
9 :     # Public License.
10 :     #
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 : efrank 1.1 #
20 :     #
21 :    
22 : efrank 1.16 # don't migrate next 4 to standard.mk since they don't make sense for kah
23 :     # I'd like to capture this into arch-dependent flags in ReleaseTools
24 :     # so both can share it.
25 : efrank 1.1
26 : olson 1.12 ARCH_BASE = $(RTROOT)/env/$(RTARCH)
27 : olson 1.20
28 :     PERL = $(shell sed -ne 's/^RTPERL=\(.*\)/\1/p' $(RTROOT)/config/RTConfig)
29 :     #PERL = $(ARCH_BASE)/bin/perl
30 : olson 1.8 CC = $(shell $(PERL) -e 'use Config; print $$Config{cc}')
31 : olson 1.12
32 : golsen 1.29 CFLAGS = $(shell $(PERL) -e 'use Config; print "$$Config{ccflags} -I$$Config{archlib}/CORE -I$(ARCH_BASE)/lib/perl5/$$Config{version}/$$Config{archname}/CORE"') -O -lm
33 : olson 1.8
34 : efrank 1.16 # define standard macros that say what we're making
35 : efrank 1.1
36 : efrank 1.16 BINPERLSCRIPTS := $(wildcard *.pl)
37 :     BINPYSCRIPTS := $(wildcard *.py)
38 : olson 1.30
39 : olson 1.31 #CEXCLUDES := fastasize.c
40 :     #CBINS = fasta_cksum.c index_contig_files.c index_sims_file.c index_translation_files.c fastasize.c compute_translation_MD5.c
41 : olson 1.30
42 : olson 1.31 CEXCLUDES := fastasize.c gjocodonlib.c gjoseqio.c gjoseqlib.c
43 :     CBINS = fasta_cksum.c index_contig_files.c index_sims_file.c index_translation_files.c fastasize.c compute_translation_MD5.c codon_counts_x_and_p.c codon_freq_eval_2.c complement_fasta.c project_codon_usage_onto_axis.c translate_fasta_6.c translate_fasta.c
44 : efrank 1.16
45 : olson 1.24 R_SCRIPTS = $(patsubst %.R,%,$(wildcard *.R))
46 : overbeek 1.22
47 :     #
48 :     # use the shscripts target so we don't have to hack the makefile infrastructure.
49 : olson 1.26 BINSHSCRIPTS := $(R_SCRIPTS) \
50 :     to_run_daily.sh \
51 : disz 1.27 to_run_new_genomes.sh \
52 : olson 1.30 run_anno_to_pubseed_flow.sh \
53 :     run_coreseed_to_pubseed_flow.sh
54 : overbeek 1.22
55 : efrank 1.16 index_contig_files: md5.c
56 :    
57 :     # I don't see how to integrate the next two into standard.mk at
58 :     # the moment because Kah does not need/use tool_hdr but fig does.
59 :     # These lines override the dot rules in standard.mk
60 : efrank 1.15
61 : olson 1.10
62 : efrank 1.3 $(bindir)/%: $(TOPDIR)/$(PKGNAME)/%.pl $(TOOL_HDR)
63 : olson 1.19 -test -f $@ && mv $@ $@.del
64 : efrank 1.2 ( cat $(TOOL_HDR) $< > $@; chmod +x $@ )
65 : olson 1.19 -test -f $@.del && rm -f $@.del
66 : efrank 1.5
67 : olson 1.7 $(bindir)/%: $(TOPDIR)/$(PKGNAME)/%.py $(TOOL_HDR_PY)
68 :     ( cat $(TOOL_HDR_PY) $< > $@; chmod +x $@ )
69 :    
70 : olson 1.23 $(bindir)/%: $(TOPDIR)/$(PKGNAME)/%.R Makefile
71 :     ( echo "#!/usr/bin/env Rscript"; cat $<) > $@; chmod +x $@
72 :    
73 : efrank 1.16 include standard.mk
74 : efrank 1.15
75 :    

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