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Revision 1.31 - (download) (annotate)
Thu Nov 14 17:26:37 2013 UTC (6 years ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2014_0912, rast_rel_2014_0729, HEAD
Changes since 1.30: +4 -4 lines
Fix the broken stuff (bob commented out some lines erroneously)

#
# Copyright (c) 2003-2006 University of Chicago and Fellowship
# for Interpretations of Genomes. All Rights Reserved.
#
# This file is part of the SEED Toolkit.
# 
# The SEED Toolkit is free software. You can redistribute
# it and/or modify it under the terms of the SEED Toolkit
# Public License. 
#
# You should have received a copy of the SEED Toolkit Public License
# along with this program; if not write to the University of Chicago
# at info@ci.uchicago.edu or the Fellowship for Interpretation of
# Genomes at veronika@thefig.info or download a copy from
# http://www.theseed.org/LICENSE.TXT.
#

#
#
#

# don't migrate next 4 to standard.mk  since they don't make sense for kah
# I'd like to capture this into arch-dependent flags in ReleaseTools
# so both can share it.

ARCH_BASE = $(RTROOT)/env/$(RTARCH)

PERL = $(shell sed -ne 's/^RTPERL=\(.*\)/\1/p' $(RTROOT)/config/RTConfig)
#PERL = $(ARCH_BASE)/bin/perl
CC =  $(shell $(PERL) -e 'use Config; print $$Config{cc}')

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

# define standard macros that say what we're making

BINPERLSCRIPTS := $(wildcard *.pl)
BINPYSCRIPTS := $(wildcard *.py)

#CEXCLUDES := fastasize.c
#CBINS = fasta_cksum.c index_contig_files.c index_sims_file.c index_translation_files.c fastasize.c compute_translation_MD5.c

CEXCLUDES := fastasize.c gjocodonlib.c gjoseqio.c gjoseqlib.c 
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

R_SCRIPTS = $(patsubst %.R,%,$(wildcard *.R))

#
# use the shscripts target so we don't have to hack the makefile infrastructure. 
BINSHSCRIPTS := $(R_SCRIPTS) \
	to_run_daily.sh \
	to_run_new_genomes.sh \
	run_anno_to_pubseed_flow.sh \
	run_coreseed_to_pubseed_flow.sh

index_contig_files: md5.c

# I don't see how to integrate the next two into standard.mk at
# the moment because Kah does not need/use tool_hdr but fig does.  
# These lines override the dot rules in standard.mk


$(bindir)/%: $(TOPDIR)/$(PKGNAME)/%.pl $(TOOL_HDR)
	-test -f $@ && mv $@ $@.del
	( cat $(TOOL_HDR) $< > $@; chmod +x $@ )
	-test -f $@.del && rm -f $@.del

$(bindir)/%: $(TOPDIR)/$(PKGNAME)/%.py $(TOOL_HDR_PY)
	( cat $(TOOL_HDR_PY) $< > $@; chmod +x $@ )

$(bindir)/%: $(TOPDIR)/$(PKGNAME)/%.R Makefile
	( echo "#!/usr/bin/env Rscript"; cat $<) > $@; chmod +x $@ 

include standard.mk



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