1# Makefile.in generated by automake 1.11.1 from Makefile.am.
2# @configure_input@
3
4# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
5# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
6# Inc.
7# This Makefile.in is free software; the Free Software Foundation
8# gives unlimited permission to copy and/or distribute it,
9# with or without modifications, as long as this notice is preserved.
10
11# This program is distributed in the hope that it will be useful,
12# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
13# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
14# PARTICULAR PURPOSE.
15
16@SET_MAKE@
17
18
19
20VPATH = @srcdir@
21pkgdatadir = $(datadir)/@PACKAGE@
22pkgincludedir = $(includedir)/@PACKAGE@
23pkglibdir = $(libdir)/@PACKAGE@
24pkglibexecdir = $(libexecdir)/@PACKAGE@
25am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
26install_sh_DATA = $(install_sh) -c -m 644
27install_sh_PROGRAM = $(install_sh) -c
28install_sh_SCRIPT = $(install_sh) -c
29INSTALL_HEADER = $(INSTALL_DATA)
30transform = $(program_transform_name)
31NORMAL_INSTALL = :
32PRE_INSTALL = :
33POST_INSTALL = :
34NORMAL_UNINSTALL = :
35PRE_UNINSTALL = :
36POST_UNINSTALL = :
37bin_PROGRAMS = bin/eufindtRNA$(EXEEXT) bin/trnascan-1.4$(EXEEXT) \
38	bin/covels-SE$(EXEEXT) bin/coves-SE$(EXEEXT)
39subdir = .
40DIST_COMMON = README $(am__configure_deps) $(dist_bin_SCRIPTS) \
41	$(include_HEADERS) $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
42	$(srcdir)/config.h.in $(top_srcdir)/configure COPYING INSTALL \
43	depcomp install-sh missing
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48am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
49 configure.lineno config.status.lineno
50mkinstalldirs = $(install_sh) -d
51CONFIG_HEADER = config.h
52CONFIG_CLEAN_FILES =
53CONFIG_CLEAN_VPATH_FILES =
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98am__install_max = 40
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113SCRIPTS = $(dist_bin_SCRIPTS)
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116am__depfiles_maybe = depfiles
117am__mv = mv -f
118COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
119	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
120CCLD = $(CC)
121LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
122SOURCES = $(bin_covels_SE_SOURCES) $(bin_coves_SE_SOURCES) \
123	$(bin_eufindtRNA_SOURCES) $(bin_trnascan_1_4_SOURCES)
124DIST_SOURCES = $(bin_covels_SE_SOURCES) $(bin_coves_SE_SOURCES) \
125	$(bin_eufindtRNA_SOURCES) $(bin_trnascan_1_4_SOURCES)
126HEADERS = $(include_HEADERS)
127ETAGS = etags
128CTAGS = ctags
129DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
130distdir = $(PACKAGE)-$(VERSION)
131top_distdir = $(distdir)
132am__remove_distdir = \
133  { test ! -d "$(distdir)" \
134    || { find "$(distdir)" -type d ! -perm -200 -exec chmod u+w {} ';' \
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136DIST_ARCHIVES = $(distdir).tar.gz
137GZIP_ENV = --best
138distuninstallcheck_listfiles = find . -type f -print
139distcleancheck_listfiles = find . -type f -print
140ACLOCAL = @ACLOCAL@
141ALLOCA = @ALLOCA@
142AMTAR = @AMTAR@
143AUTOCONF = @AUTOCONF@
144AUTOHEADER = @AUTOHEADER@
145AUTOMAKE = @AUTOMAKE@
146AWK = @AWK@
147CC = @CC@
148CCDEPMODE = @CCDEPMODE@
149CFLAGS = @CFLAGS@
150CPP = @CPP@
151CPPFLAGS = @CPPFLAGS@
152CYGPATH_W = @CYGPATH_W@
153DEFS = @DEFS@
154DEPDIR = @DEPDIR@
155ECHO_C = @ECHO_C@
156ECHO_N = @ECHO_N@
157ECHO_T = @ECHO_T@
158EGREP = @EGREP@
159EXEEXT = @EXEEXT@
160GREP = @GREP@
161INSTALL = @INSTALL@
162INSTALL_DATA = @INSTALL_DATA@
163INSTALL_PROGRAM = @INSTALL_PROGRAM@
164INSTALL_SCRIPT = @INSTALL_SCRIPT@
165INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
166LDFLAGS = @LDFLAGS@
167LIBOBJS = @LIBOBJS@
168LIBS = @LIBS@
169LTLIBOBJS = @LTLIBOBJS@
170MAKEINFO = @MAKEINFO@
171MKDIR_P = @MKDIR_P@
172OBJEXT = @OBJEXT@
173PACKAGE = @PACKAGE@
174PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
175PACKAGE_NAME = @PACKAGE_NAME@
176PACKAGE_STRING = @PACKAGE_STRING@
177PACKAGE_TARNAME = @PACKAGE_TARNAME@
178PACKAGE_URL = @PACKAGE_URL@
179PACKAGE_VERSION = @PACKAGE_VERSION@
180PATH_SEPARATOR = @PATH_SEPARATOR@
181PERL = @PERL@
182SET_MAKE = @SET_MAKE@
183SHELL = @SHELL@
184STRIP = @STRIP@
185VERSION = @VERSION@
186abs_builddir = @abs_builddir@
187abs_srcdir = @abs_srcdir@
188abs_top_builddir = @abs_top_builddir@
189abs_top_srcdir = @abs_top_srcdir@
190ac_ct_CC = @ac_ct_CC@
191am__include = @am__include@
192am__leading_dot = @am__leading_dot@
193am__quote = @am__quote@
194am__tar = @am__tar@
195am__untar = @am__untar@
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197build_alias = @build_alias@
198builddir = @builddir@
199datadir = @datadir@
200datarootdir = @datarootdir@
201docdir = @docdir@
202dvidir = @dvidir@
203exec_prefix = @exec_prefix@
204host_alias = @host_alias@
205htmldir = @htmldir@
206includedir = @includedir@
207infodir = @infodir@
208install_sh = @install_sh@
209libdir = @libdir@
210libexecdir = @libexecdir@
211localedir = @localedir@
212localstatedir = @localstatedir@
213mandir = @mandir@
214mkdir_p = @mkdir_p@
215oldincludedir = @oldincludedir@
216pdfdir = @pdfdir@
217prefix = @prefix@
218program_transform_name = @program_transform_name@
219psdir = @psdir@
220sbindir = @sbindir@
221sharedstatedir = @sharedstatedir@
222srcdir = @srcdir@
223sysconfdir = @sysconfdir@
224target_alias = @target_alias@
225top_build_prefix = @top_build_prefix@
226top_builddir = @top_builddir@
227top_srcdir = @top_srcdir@
228
229# not a GNU package
230# build object files in their source location
231AUTOMAKE_OPTIONS = foreign subdir-objects
232
233# set flags
234AM_CFLAGS = -O
235LDADD = -lm
236
237# macros for program dependencies
238EUFIND = src/eufind_const.h src/eufind_main.c src/pavesi.c
239SQUIDUTILS = src/seqstat_main.c src/reformat_main.c src/shuffle_main.c src/revcomp_main.c src/getopt.c
240SQUIDSRC = src/alignio.c src/sqerror.c src/sqio.c src/iupac.c src/msf.c src/revcomp.c src/selex.c src/sre_ctype.c src/sre_math.c src/sre_string.c src/stack.c src/types.c src/gnuregex.c src/interleaved.c src/getopt.c
241SQUIDHDRS = src/squid.h src/sqfuncs.h src/gnuregex.h
242COVEMAIN = src/align_main.c src/build_main.c src/emit_main.c src/learnprior_main.c src/train_main.c src/scan_main.c src/score_main.c src/structcheck_main.c
243COVESRC = src/align.c src/dbviterbi.c src/debug.c src/emit.c src/fast-dbviterbi.c src/fastmodelmaker.c src/konings.c src/lengthdist.c src/maxmodelmaker.c src/misc.c src/model.c src/modelmaking.c src/prior.c src/probify.c src/save.c src/smallviterbi.c src/scorestack.c src/structs.c src/trace.c src/viterbi.c $(SQUIDSRC)
244bin_eufindtRNA_SOURCES = $(SQUIDHDRS) $(SQUIDSRC) $(EUFIND)
245bin_trnascan_1_4_SOURCES = src/trnascan.c
246bin_trnascan_1_4_CFLAGS = -DTSCANDIR=\"$(libdir)\/tRNAscan-SE\/models\"  $(AM_CFLAGS)
247bin_covels_SE_SOURCES = $(COVESRC) src/scan_main.c
248bin_coves_SE_SOURCES = $(COVESRC) src/score_main.c
249
250# process scripts
251# treat tRNAscan-SE.conf as a script since it's just easier
252dist_bin_SCRIPTS = bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter tRNAscan-SE tRNAscan-SE.conf
253# for a few files, need to substitute perl path, bin directory, and lib directory
254# first, define a function for it
255do_subst = sed -e 's,\@bindir\@,$(bindir),g' -e 's,\@libdir\@,$(libdir),g' -e 's,[@]PERL[@],$(PERL),g' -e 's,\@INFERNAL\@,$(INFERNAL),g'
256
257# extra steps for cleaning/distribution
258CLEANFILES = $(dist_bin_SCRIPTS) $(srcdir)/lib/*
259include_HEADERS = $(srcdir)/src/*.h
260EXTRA_DIST = lib src/sstofa.in src/fasta2gsi.in EukHighConfidenceFilter.in tRNAscan-SE.src tRNAscan-SE.conf.src
261all: config.h
262	$(MAKE) $(AM_MAKEFLAGS) all-am
263
264.SUFFIXES:
265.SUFFIXES: .c .o .obj
266am--refresh:
267	@:
268$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
269	@for dep in $?; do \
270	  case '$(am__configure_deps)' in \
271	    *$$dep*) \
272	      echo ' cd $(srcdir) && $(AUTOMAKE) --foreign'; \
273	      $(am__cd) $(srcdir) && $(AUTOMAKE) --foreign \
274		&& exit 0; \
275	      exit 1;; \
276	  esac; \
277	done; \
278	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign Makefile'; \
279	$(am__cd) $(top_srcdir) && \
280	  $(AUTOMAKE) --foreign Makefile
281.PRECIOUS: Makefile
282Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
283	@case '$?' in \
284	  *config.status*) \
285	    echo ' $(SHELL) ./config.status'; \
286	    $(SHELL) ./config.status;; \
287	  *) \
288	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe)'; \
289	    cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe);; \
290	esac;
291
292$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
293	$(SHELL) ./config.status --recheck
294
295$(top_srcdir)/configure:  $(am__configure_deps)
296	$(am__cd) $(srcdir) && $(AUTOCONF)
297$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
298	$(am__cd) $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS)
299$(am__aclocal_m4_deps):
300
301config.h: stamp-h1
302	@if test ! -f $@; then \
303	  rm -f stamp-h1; \
304	  $(MAKE) $(AM_MAKEFLAGS) stamp-h1; \
305	else :; fi
306
307stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status
308	@rm -f stamp-h1
309	cd $(top_builddir) && $(SHELL) ./config.status config.h
310$(srcdir)/config.h.in:  $(am__configure_deps)
311	($(am__cd) $(top_srcdir) && $(AUTOHEADER))
312	rm -f stamp-h1
313	touch $@
314
315distclean-hdr:
316	-rm -f config.h stamp-h1
317install-binPROGRAMS: $(bin_PROGRAMS)
318	@$(NORMAL_INSTALL)
319	test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
320	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
321	for p in $$list; do echo "$$p $$p"; done | \
322	sed 's/$(EXEEXT)$$//' | \
323	while read p p1; do if test -f $$p; \
324	  then echo "$$p"; echo "$$p"; else :; fi; \
325	done | \
326	sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
327	    -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
328	sed 'N;N;N;s,\n, ,g' | \
329	$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
330	  { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
331	    if ($$2 == $$4) files[d] = files[d] " " $$1; \
332	    else { print "f", $$3 "/" $$4, $$1; } } \
333	  END { for (d in files) print "f", d, files[d] }' | \
334	while read type dir files; do \
335	    if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
336	    test -z "$$files" || { \
337	      echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \
338	      $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
339	    } \
340	; done
341
342uninstall-binPROGRAMS:
343	@$(NORMAL_UNINSTALL)
344	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
345	files=`for p in $$list; do echo "$$p"; done | \
346	  sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
347	      -e 's/$$/$(EXEEXT)/' `; \
348	test -n "$$list" || exit 0; \
349	echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
350	cd "$(DESTDIR)$(bindir)" && rm -f $$files
351
352clean-binPROGRAMS:
353	-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
354src/$(am__dirstamp):
355	@$(MKDIR_P) src
356	@: > src/$(am__dirstamp)
357src/$(DEPDIR)/$(am__dirstamp):
358	@$(MKDIR_P) src/$(DEPDIR)
359	@: > src/$(DEPDIR)/$(am__dirstamp)
360src/align.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
361src/dbviterbi.$(OBJEXT): src/$(am__dirstamp) \
362	src/$(DEPDIR)/$(am__dirstamp)
363src/debug.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
364src/emit.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
365src/fast-dbviterbi.$(OBJEXT): src/$(am__dirstamp) \
366	src/$(DEPDIR)/$(am__dirstamp)
367src/fastmodelmaker.$(OBJEXT): src/$(am__dirstamp) \
368	src/$(DEPDIR)/$(am__dirstamp)
369src/konings.$(OBJEXT): src/$(am__dirstamp) \
370	src/$(DEPDIR)/$(am__dirstamp)
371src/lengthdist.$(OBJEXT): src/$(am__dirstamp) \
372	src/$(DEPDIR)/$(am__dirstamp)
373src/maxmodelmaker.$(OBJEXT): src/$(am__dirstamp) \
374	src/$(DEPDIR)/$(am__dirstamp)
375src/misc.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
376src/model.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
377src/modelmaking.$(OBJEXT): src/$(am__dirstamp) \
378	src/$(DEPDIR)/$(am__dirstamp)
379src/prior.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
380src/probify.$(OBJEXT): src/$(am__dirstamp) \
381	src/$(DEPDIR)/$(am__dirstamp)
382src/save.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
383src/smallviterbi.$(OBJEXT): src/$(am__dirstamp) \
384	src/$(DEPDIR)/$(am__dirstamp)
385src/scorestack.$(OBJEXT): src/$(am__dirstamp) \
386	src/$(DEPDIR)/$(am__dirstamp)
387src/structs.$(OBJEXT): src/$(am__dirstamp) \
388	src/$(DEPDIR)/$(am__dirstamp)
389src/trace.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
390src/viterbi.$(OBJEXT): src/$(am__dirstamp) \
391	src/$(DEPDIR)/$(am__dirstamp)
392src/alignio.$(OBJEXT): src/$(am__dirstamp) \
393	src/$(DEPDIR)/$(am__dirstamp)
394src/sqerror.$(OBJEXT): src/$(am__dirstamp) \
395	src/$(DEPDIR)/$(am__dirstamp)
396src/sqio.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
397src/iupac.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
398src/msf.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
399src/revcomp.$(OBJEXT): src/$(am__dirstamp) \
400	src/$(DEPDIR)/$(am__dirstamp)
401src/selex.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
402src/sre_ctype.$(OBJEXT): src/$(am__dirstamp) \
403	src/$(DEPDIR)/$(am__dirstamp)
404src/sre_math.$(OBJEXT): src/$(am__dirstamp) \
405	src/$(DEPDIR)/$(am__dirstamp)
406src/sre_string.$(OBJEXT): src/$(am__dirstamp) \
407	src/$(DEPDIR)/$(am__dirstamp)
408src/stack.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
409src/types.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
410src/gnuregex.$(OBJEXT): src/$(am__dirstamp) \
411	src/$(DEPDIR)/$(am__dirstamp)
412src/interleaved.$(OBJEXT): src/$(am__dirstamp) \
413	src/$(DEPDIR)/$(am__dirstamp)
414src/getopt.$(OBJEXT): src/$(am__dirstamp) \
415	src/$(DEPDIR)/$(am__dirstamp)
416src/scan_main.$(OBJEXT): src/$(am__dirstamp) \
417	src/$(DEPDIR)/$(am__dirstamp)
418bin/$(am__dirstamp):
419	@$(MKDIR_P) bin
420	@: > bin/$(am__dirstamp)
421bin/covels-SE$(EXEEXT): $(bin_covels_SE_OBJECTS) $(bin_covels_SE_DEPENDENCIES) bin/$(am__dirstamp)
422	@rm -f bin/covels-SE$(EXEEXT)
423	$(LINK) $(bin_covels_SE_OBJECTS) $(bin_covels_SE_LDADD) $(LIBS)
424src/score_main.$(OBJEXT): src/$(am__dirstamp) \
425	src/$(DEPDIR)/$(am__dirstamp)
426bin/coves-SE$(EXEEXT): $(bin_coves_SE_OBJECTS) $(bin_coves_SE_DEPENDENCIES) bin/$(am__dirstamp)
427	@rm -f bin/coves-SE$(EXEEXT)
428	$(LINK) $(bin_coves_SE_OBJECTS) $(bin_coves_SE_LDADD) $(LIBS)
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780	       && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" uninstall \
781	       && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" \
782	            distuninstallcheck_dir="$$dc_destdir" distuninstallcheck; \
783	      } || { rm -rf "$$dc_destdir"; exit 1; }) \
784	  && rm -rf "$$dc_destdir" \
785	  && $(MAKE) $(AM_MAKEFLAGS) dist \
786	  && rm -rf $(DIST_ARCHIVES) \
787	  && $(MAKE) $(AM_MAKEFLAGS) distcleancheck \
788	  && cd "$$am__cwd" \
789	  || exit 1
790	$(am__remove_distdir)
791	@(echo "$(distdir) archives ready for distribution: "; \
792	  list='$(DIST_ARCHIVES)'; for i in $$list; do echo $$i; done) | \
793	  sed -e 1h -e 1s/./=/g -e 1p -e 1x -e '$$p' -e '$$x'
794distuninstallcheck:
795	@$(am__cd) '$(distuninstallcheck_dir)' \
796	&& test `$(distuninstallcheck_listfiles) | wc -l` -le 1 \
797	   || { echo "ERROR: files left after uninstall:" ; \
798	        if test -n "$(DESTDIR)"; then \
799	          echo "  (check DESTDIR support)"; \
800	        fi ; \
801	        $(distuninstallcheck_listfiles) ; \
802	        exit 1; } >&2
803distcleancheck: distclean
804	@if test '$(srcdir)' = . ; then \
805	  echo "ERROR: distcleancheck can only run from a VPATH build" ; \
806	  exit 1 ; \
807	fi
808	@test `$(distcleancheck_listfiles) | wc -l` -eq 0 \
809	  || { echo "ERROR: files left in build directory after distclean:" ; \
810	       $(distcleancheck_listfiles) ; \
811	       exit 1; } >&2
812check-am: all-am
813check: check-am
814all-am: Makefile $(PROGRAMS) $(SCRIPTS) $(HEADERS) config.h
815installdirs:
816	for dir in "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)" "$(DESTDIR)$(includedir)"; do \
817	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
818	done
819install: install-am
820install-exec: install-exec-am
821install-data: install-data-am
822uninstall: uninstall-am
823
824install-am: all-am
825	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
826
827installcheck: installcheck-am
828install-strip:
829	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
830	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
831	  `test -z '$(STRIP)' || \
832	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
833mostlyclean-generic:
834
835clean-generic:
836	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
837
838distclean-generic:
839	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
840	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
841	-rm -f bin/$(am__dirstamp)
842	-rm -f src/$(DEPDIR)/$(am__dirstamp)
843	-rm -f src/$(am__dirstamp)
844
845maintainer-clean-generic:
846	@echo "This command is intended for maintainers to use"
847	@echo "it deletes files that may require special tools to rebuild."
848clean: clean-am
849
850clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
851
852distclean: distclean-am
853	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
854	-rm -rf src/$(DEPDIR)
855	-rm -f Makefile
856distclean-am: clean-am distclean-compile distclean-generic \
857	distclean-hdr distclean-tags
858
859dvi: dvi-am
860
861dvi-am:
862
863html: html-am
864
865html-am:
866
867info: info-am
868
869info-am:
870
871install-data-am: install-includeHEADERS
872	@$(NORMAL_INSTALL)
873	$(MAKE) $(AM_MAKEFLAGS) install-data-hook
874install-dvi: install-dvi-am
875
876install-dvi-am:
877
878install-exec-am: install-binPROGRAMS install-dist_binSCRIPTS
879
880install-html: install-html-am
881
882install-html-am:
883
884install-info: install-info-am
885
886install-info-am:
887
888install-man:
889
890install-pdf: install-pdf-am
891
892install-pdf-am:
893
894install-ps: install-ps-am
895
896install-ps-am:
897
898installcheck-am:
899
900maintainer-clean: maintainer-clean-am
901	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
902	-rm -rf $(top_srcdir)/autom4te.cache
903	-rm -rf src/$(DEPDIR)
904	-rm -f Makefile
905maintainer-clean-am: distclean-am maintainer-clean-generic
906
907mostlyclean: mostlyclean-am
908
909mostlyclean-am: mostlyclean-compile mostlyclean-generic
910
911pdf: pdf-am
912
913pdf-am:
914
915ps: ps-am
916
917ps-am:
918
919uninstall-am: uninstall-binPROGRAMS uninstall-dist_binSCRIPTS \
920	uninstall-includeHEADERS
921	@$(NORMAL_INSTALL)
922	$(MAKE) $(AM_MAKEFLAGS) uninstall-hook
923.MAKE: all install-am install-data-am install-strip uninstall-am
924
925.PHONY: CTAGS GTAGS all all-am am--refresh check check-am clean \
926	clean-binPROGRAMS clean-generic ctags dist dist-all dist-bzip2 \
927	dist-gzip dist-lzma dist-shar dist-tarZ dist-xz dist-zip \
928	distcheck distclean distclean-compile distclean-generic \
929	distclean-hdr distclean-tags distcleancheck distdir \
930	distuninstallcheck dvi dvi-am html html-am info info-am \
931	install install-am install-binPROGRAMS install-data \
932	install-data-am install-data-hook install-dist_binSCRIPTS \
933	install-dvi install-dvi-am install-exec install-exec-am \
934	install-html install-html-am install-includeHEADERS \
935	install-info install-info-am install-man install-pdf \
936	install-pdf-am install-ps install-ps-am install-strip \
937	installcheck installcheck-am installdirs maintainer-clean \
938	maintainer-clean-generic mostlyclean mostlyclean-compile \
939	mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
940	uninstall-am uninstall-binPROGRAMS uninstall-dist_binSCRIPTS \
941	uninstall-hook uninstall-includeHEADERS
942
943
944# then create build rules
945
946tRNAscan-SE: tRNAscan-SE.src Makefile
947	$(do_subst) < $(srcdir)/tRNAscan-SE.src > tRNAscan-SE
948	chmod +x tRNAscan-SE
949
950tRNAscan-SE.conf: tRNAscan-SE.conf.src Makefile
951	$(do_subst) < $(srcdir)/tRNAscan-SE.conf.src > tRNAscan-SE.conf
952	chmod +x tRNAscan-SE.conf
953
954bin/sstofa: src/sstofa.in Makefile
955	$(do_subst) < $(srcdir)/src/sstofa.in > bin/sstofa
956	chmod +x bin/sstofa
957
958bin/fasta2gsi: src/fasta2gsi.in Makefile
959	$(do_subst) < $(srcdir)/src/fasta2gsi.in > bin/fasta2gsi
960	chmod +x bin/fasta2gsi
961
962bin/EukHighConfidenceFilter: EukHighConfidenceFilter.in Makefile
963	$(do_subst) < $(srcdir)/EukHighConfidenceFilter.in > bin/EukHighConfidenceFilter
964	chmod +x bin/EukHighConfidenceFilter
965
966# copy libraries. We don't have "libraries" in the libgmp.so.4 kind, but we do have data libraries, so we don't have to deal with lib_LTLIBRARIES.
967install-data-hook:
968	chmod u+w $(exec_prefix)
969	test -d $(libdir) || mkdir $(libdir)
970	chmod u+w $(libdir)
971	test -d $(libdir)/tRNAscan-SE || mkdir $(libdir)/tRNAscan-SE
972	cp -rf $(srcdir)/lib/* $(libdir)/tRNAscan-SE
973
974# remove lib/ files during uninstallation. A bit of a hack, since lib files are write-protected by default. Files
975uninstall-hook:
976	chmod -R u+w $(libdir)/tRNAscan-SE
977	rm -rf $(libdir)/tRNAscan-SE
978
979# Tell versions [3.59,3.63) of GNU make to not export all variables.
980# Otherwise a system limit (for SysV at least) may be exceeded.
981.NOEXPORT:
982