# Makefile.in generated by automake 1.11.1 from Makefile.am.
# @configure_input@

# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
# Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE.

@SET_MAKE@

VPATH = @srcdir@
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
pkglibexecdir = $(libexecdir)/@PACKAGE@
am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
install_sh_DATA = $(install_sh) -c -m 644
install_sh_PROGRAM = $(install_sh) -c
install_sh_SCRIPT = $(install_sh) -c
INSTALL_HEADER = $(INSTALL_DATA)
transform = $(program_transform_name)
NORMAL_INSTALL = :
PRE_INSTALL = :
POST_INSTALL = :
NORMAL_UNINSTALL = :
PRE_UNINSTALL = :
POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@

# WEBSITE OR WEBSERVICE
@WEBSITE_TRUE@am__append_1 = $(DUALUSE_SERVICES)
@WEBSERVICE_TRUE@@WEBSITE_FALSE@am__append_2 = $(DUALUSE_SERVICES)
@WEBSERVICE_TRUE@am__append_3 = $(WEBSERVICE_SERVICES)
@WEBSITE_TRUE@am__append_4 = $(WEBSITE_WEBUTILS)
subdir = scripts
DIST_COMMON = README $(srcdir)/Makefile.am $(srcdir)/Makefile.in
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am__aclocal_m4_deps = $(top_srcdir)/configure.ac
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CONFIG_HEADER = $(top_builddir)/config.h
CONFIG_CLEAN_FILES =
CONFIG_CLEAN_VPATH_FILES =
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am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(perlmoddir)"
SCRIPTS = $(bin_SCRIPTS) $(perlmod_SCRIPTS)
SOURCES =
DIST_SOURCES =
am__tty_colors = \
red=; grn=; lgn=; blu=; std=
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
ANT = @ANT@
AR = @AR@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
AWK = @AWK@
BLOCKS_URL = @BLOCKS_URL@
CC = @CC@
CCDEPMODE = @CCDEPMODE@
CFLAGS = @CFLAGS@
CONTACT = @CONTACT@
CONVERT = @CONVERT@
CPP = @CPP@
CPPFLAGS = @CPPFLAGS@
CYGPATH_W = @CYGPATH_W@
DEBUG_FLAGS = @DEBUG_FLAGS@
DEFS = @DEFS@
DEPDIR = @DEPDIR@
DLLTOOL = @DLLTOOL@
DSYMUTIL = @DSYMUTIL@
DUMPBIN = @DUMPBIN@
ECHO_C = @ECHO_C@
ECHO_N = @ECHO_N@
ECHO_T = @ECHO_T@
EGREP = @EGREP@
EXEEXT = @EXEEXT@
FGREP = @FGREP@
GHOSTSCRIPT = @GHOSTSCRIPT@
GOSERVER_URL = @GOSERVER_URL@
GREP = @GREP@
HAVE_ELINKS = @HAVE_ELINKS@
HOSTNAME = @HOSTNAME@
INSTALL = @INSTALL@
INSTALL_DATA = @INSTALL_DATA@
INSTALL_PROGRAM = @INSTALL_PROGRAM@
INSTALL_SCRIPT = @INSTALL_SCRIPT@
INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
LAMBIN = @LAMBIN@
LD = @LD@
LDFLAGS = @LDFLAGS@
LIBEXSLT_CFLAGS = @LIBEXSLT_CFLAGS@
LIBEXSLT_LIBS = @LIBEXSLT_LIBS@
LIBOBJS = @LIBOBJS@
LIBS = @LIBS@
LIBTOOL = @LIBTOOL@
LIBXML2_CFLAGS = @LIBXML2_CFLAGS@
LIBXML2_LIBS = @LIBXML2_LIBS@
LIBXSLT_CFLAGS = @LIBXSLT_CFLAGS@
LIBXSLT_LIBS = @LIBXSLT_LIBS@
LIPO = @LIPO@
LN_S = @LN_S@
LTLIBOBJS = @LTLIBOBJS@
MACHID = @MACHID@
MAIL = @MAIL@
MAKEINFO = @MAKEINFO@
MANIFEST_TOOL = @MANIFEST_TOOL@
MAST_PORT = @MAST_PORT@
MAXTIME = @MAXTIME@
MEME_DB = @MEME_DB@
MEME_DIRECTORY = @MEME_DIRECTORY@
MEME_LOGS = @MEME_LOGS@
MEME_PORT = @MEME_PORT@
MEME_TEMP = @MEME_TEMP@
MKDIR_P = @MKDIR_P@
MPICC = @MPICC@
MPIFLAGS = @MPIFLAGS@
MPIINC = @MPIINC@
MPILIBDIR = @MPILIBDIR@
MPITYPE = @MPITYPE@
MPI_CMD = @MPI_CMD@
NM = @NM@
NMEDIT = @NMEDIT@
OBJDUMP = @OBJDUMP@
OBJEXT = @OBJEXT@
OPAL_URL = @OPAL_URL@
OPAL_XML = @OPAL_XML@
OPT_FLAGS = @OPT_FLAGS@
OTOOL = @OTOOL@
OTOOL64 = @OTOOL64@
PACKAGE = @PACKAGE@
PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
PACKAGE_NAME = @PACKAGE_NAME@
PACKAGE_STRING = @PACKAGE_STRING@
PACKAGE_TARNAME = @PACKAGE_TARNAME@
PACKAGE_URL = @PACKAGE_URL@
PACKAGE_VERSION = @PACKAGE_VERSION@
PATH_SEPARATOR = @PATH_SEPARATOR@
PERL = @PERL@
PYTHON = @PYTHON@
RANLIB = @RANLIB@
SED = @SED@
SENDMAIL = @SENDMAIL@
SET_MAKE = @SET_MAKE@
SHELL = @SHELL@
STRIP = @STRIP@
URL = @URL@
VERSION = @VERSION@
WEBDIR = @WEBDIR@
WEBSERVICE = @WEBSERVICE@
XML2_CONFIG = @XML2_CONFIG@
XSLT_CONFIG = @XSLT_CONFIG@
abs_builddir = @abs_builddir@
abs_srcdir = @abs_srcdir@
abs_top_builddir = @abs_top_builddir@
abs_top_srcdir = @abs_top_srcdir@
ac_ct_AR = @ac_ct_AR@
ac_ct_CC = @ac_ct_CC@
ac_ct_DUMPBIN = @ac_ct_DUMPBIN@
am__include = @am__include@
am__leading_dot = @am__leading_dot@
am__quote = @am__quote@
am__tar = @am__tar@
am__untar = @am__untar@
bindir = @bindir@
build = @build@
build_alias = @build_alias@
build_cpu = @build_cpu@
build_os = @build_os@
build_vendor = @build_vendor@
builddir = @builddir@
datadir = @datadir@
datarootdir = @datarootdir@
docdir = @docdir@
dvidir = @dvidir@
exec_prefix = @exec_prefix@
host = @host@
host_alias = @host_alias@
host_cpu = @host_cpu@
host_os = @host_os@
host_vendor = @host_vendor@
htmldir = @htmldir@
includedir = @includedir@
infodir = @infodir@
install_sh = @install_sh@
libdir = @libdir@
libexecdir = @libexecdir@
localedir = @localedir@
localstatedir = @localstatedir@
mandir = @mandir@
mkdir_p = @mkdir_p@
oldincludedir = @oldincludedir@
pdfdir = @pdfdir@
prefix = @prefix@
program_transform_name = @program_transform_name@
psdir = @psdir@
sbindir = @sbindir@
sharedstatedir = @sharedstatedir@
srcdir = @srcdir@
sysconfdir = @sysconfdir@
target_alias = @target_alias@
top_build_prefix = @top_build_prefix@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
@WEBSITE_FALSE@MEME_DOC_DIR = $(prefix)/doc

# Set installation location for doc files.
@WEBSITE_TRUE@MEME_DOC_DIR = $(WEBDIR)/doc
ARCHIVE_REVISION = $(shell cat ../ARCHIVE_REVISION)
ARCHIVE_DATE = $(shell cat ../ARCHIVE_DATE)
SEDSPEC = \
	-e 's%@ARCHIVE_REVISION@%$(ARCHIVE_REVISION)%' \
	-e 's%@ARCHIVE_DATE@%$(ARCHIVE_DATE)%' \
	-e 's%@ARCHIVE_VERSION@%$(VERSION)%' \
	-e 's%@WEB_DIR@%$(WEBDIR)%' \
	-e 's%@TMP_DIR@%$(MEME_TEMP)%' \
	-e 's%@WHICHPERL@%$(PERL)%' \
	-e 's%@WHICHCONVERT@%$(CONVERT)%' \
	-e 's%@WHICHGHOSTSCRIPT@%$(GHOSTSCRIPT)%' \
	-e 's%@PERLMODDIR@%$(perlmoddir)%' \
	-e 's%@PERLLIBDIR@%$(libdir)/perl%' \
	-e 's%@WHICHPYTHON@%$(PYTHON)%' \
	-e 's%@WHICHGHOSTSCRIPT@%$(GHOSTSCRIPT)%' \
	-e 's%@MACH_ID@%$(MACHID)%' \
	-e 's%@sendmail@%$(SENDMAIL)%' \
	-e 's%@mail@%$(MAIL)%' \
	-e 's%\@CONTACT\@%$(CONTACT)%' \
	-e 's%@LAM_BIN@%$(LAMBIN)%' \
	-e 's%@MPICMD@%$(MPI_CMD)%' \
	-e 's%@MEMEDIR@%$(MEME_DIRECTORY)%' \
	-e 's%@MEME_ETC_DIR@%$(top_srcdir)/etc%' \
	-e 's%@APPCONFIGDIR@%$(sysconfdir)%' \
	-e 's%@BINDIR@%$(bindir)%' \
	-e 's%@MEMELOGS@%$(MEME_LOGS)%' \
	-e 's%@MEMEDB@%$(MEME_DB)%' \
	-e 's%@HOST_NAME@%$(HOSTNAME)%' \
	-e 's%@MEMEUSER@%$(MEME_USER)%' \
	-e 's%@MPI_TYPE@%$(MPITYPE)%' \
	-e 's%@S_VERSION@%$(VERSION)%' \
	-e 's%@SITE_URL@%$(URL)%' \
	-e 's%@OPAL@%$(OPAL_URL)%' \
	-e 's%@DOCDIR@%$(MEME_DOC_DIR)/%'

BUILT_PERL_MOD = MemeWebUtils.pm convert2html.pl
perlmoddir = $(libdir)/perl
perlmod_SCRIPTS = $(BUILT_PERL_MOD) ExecUtils.pm MotifUtils.pm CatList.pm
MEME_TESTS = runcheck metatest
@PARALLEL_TRUE@PARALLEL_TESTS = runcheck_p
INPUT_FILES = $(wildcard *.in)
BUILT_UTILS = \
  ama-qvalues \
  beeml2meme \
  cat_max \
  compare_dates \
  dreme \
  fasta-center \
  fasta-dinucleotide-shuffle \
  fasta-dinucleotide-shuffle.py \
  fasta-fetch \
  fasta-get-markov \
  fasta-hamming-enrich \
  fasta-hamming-enrich.py \
  fasta-make-index \
  fasta-shuffle-letters \
  fasta-subsample \
  fasta-unique-names \
  glam2html \
  glam2psfm \
  glam2scan2html \
  get_db_csv \
  chen2meme \
  jaspar2meme \
  hart2meme-bkg \
  hartemink2psp \
  iupac2meme \
  meme \
  meme-chip \
  meme-get-motif \
  meme2meme \
  mhmm2html \
  nmica2meme \
  priority2meme \
  psp-gen \
  rna2meme \
  scpd2meme \
  taipale2meme \
  tamo2meme \
  transfac2meme \
  uniprobe2meme \
  update_db

UTILS = \
  download \
  hypergeometric.py \
  plotgen \
  prior_utils.pl \
  read_fasta_file.pl \
  sd \
  sequence.py \
  update_meme_tests \
  $(BUILT_UTILS)


# services
DUALUSE_SERVICES = \
  tomtom_webservice

WEBSERVICE_SERVICES = \
  centrimo_webservice \
  dreme_webservice \
  fimo_webservice \
  glam2scan_webservice \
  glam2_webservice \
  gomo_webservice \
  mast_webservice \
  mcast_webservice \
  meme-chip_webservice \
  meme_webservice \
  spamo_webservice


#utilities
WEBSITE_BUILT_WEBUTILS = \
  lrun \
  mailer \
  update-plot-usage

WEBSITE_WEBUTILS = \
  plot-usage \
  texit \
  usage-reports \
  $(WEBSITE_BUILT_WEBUTILS)

MEME_SERVICES = $(am__append_1) $(am__append_2) $(am__append_3)
MEME_WEBUTILS = $(am__append_4)

# Set automake targets
TESTS_ENVIRONMENT = testdir=$(top_srcdir)/tests
TESTS = $(MEME_TESTS) $(PARALLEL_TESTS)
bin_SCRIPTS = $(UTILS) $(MEME_WEBUTILS) $(MEME_SERVICES)
svndir = $(prefix)

# Define which files to delete if target is 'make clean'.
CLEANFILES = \
  $(BUILT_PERL_MOD) \
  $(BUILT_UTILS) \
  $(WEBSITE_BUILT_WEBUTILS) \
  $(MEME_SERVICES) \
  metatest

EXTRA_DIST = \
  CatList.pm \
  comb-dynamicprog.pl \
  dependencies.pl \
  DiffXML.pm \
  download \
  ExecUtils.pm \
  hypergeometric.py \
  hypergeometric-dynamicprog.pl \
  MotifUtils.pm \
  obo2dag.jar \
  plotgen \
  plot-usage \
  prior_utils.pl \
  read_fasta_file.pl \
  runcheck \
  runtests \
  sd \
  sequence.py \
  texit \
  update_meme_tests \
  usage-reports \
  $(INPUT_FILES)

all: all-am

.SUFFIXES:
.SUFFIXES: .old .svnignore
$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
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Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
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$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
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$(top_srcdir)/configure:  $(am__configure_deps)
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$(am__aclocal_m4_deps):
install-binSCRIPTS: $(bin_SCRIPTS)
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	test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
	@list='$(bin_SCRIPTS)'; test -n "$(bindir)" || list=; \
	for p in $$list; do \
	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
	  if test -f "$$d$$p"; then echo "$$d$$p"; echo "$$p"; else :; fi; \
	done | \
	sed -e 'p;s,.*/,,;n' \
	    -e 'h;s|.*|.|' \
	    -e 'p;x;s,.*/,,;$(transform)' | sed 'N;N;N;s,\n, ,g' | \
	$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1; } \
	  { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
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	      if (++n[d] == $(am__install_max)) { \
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	while read type dir files; do \
	     if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
	     test -z "$$files" || { \
	       echo " $(INSTALL_SCRIPT) $$files '$(DESTDIR)$(bindir)$$dir'"; \
	       $(INSTALL_SCRIPT) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
	     } \
	; done

uninstall-binSCRIPTS:
	@$(NORMAL_UNINSTALL)
	@list='$(bin_SCRIPTS)'; test -n "$(bindir)" || exit 0; \
	files=`for p in $$list; do echo "$$p"; done | \
	       sed -e 's,.*/,,;$(transform)'`; \
	test -n "$$list" || exit 0; \
	echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
	cd "$(DESTDIR)$(bindir)" && rm -f $$files
install-perlmodSCRIPTS: $(perlmod_SCRIPTS)
	@$(NORMAL_INSTALL)
	test -z "$(perlmoddir)" || $(MKDIR_P) "$(DESTDIR)$(perlmoddir)"
	@list='$(perlmod_SCRIPTS)'; test -n "$(perlmoddir)" || list=; \
	for p in $$list; do \
	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
	  if test -f "$$d$$p"; then echo "$$d$$p"; echo "$$p"; else :; fi; \
	done | \
	sed -e 'p;s,.*/,,;n' \
	    -e 'h;s|.*|.|' \
	    -e 'p;x;s,.*/,,;$(transform)' | sed 'N;N;N;s,\n, ,g' | \
	$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1; } \
	  { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
	    if ($$2 == $$4) { files[d] = files[d] " " $$1; \
	      if (++n[d] == $(am__install_max)) { \
		print "f", d, files[d]; n[d] = 0; files[d] = "" } } \
	    else { print "f", d "/" $$4, $$1 } } \
	  END { for (d in files) print "f", d, files[d] }' | \
	while read type dir files; do \
	     if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
	     test -z "$$files" || { \
	       echo " $(INSTALL_SCRIPT) $$files '$(DESTDIR)$(perlmoddir)$$dir'"; \
	       $(INSTALL_SCRIPT) $$files "$(DESTDIR)$(perlmoddir)$$dir" || exit $$?; \
	     } \
	; done

uninstall-perlmodSCRIPTS:
	@$(NORMAL_UNINSTALL)
	@list='$(perlmod_SCRIPTS)'; test -n "$(perlmoddir)" || exit 0; \
	files=`for p in $$list; do echo "$$p"; done | \
	       sed -e 's,.*/,,;$(transform)'`; \
	test -n "$$list" || exit 0; \
	echo " ( cd '$(DESTDIR)$(perlmoddir)' && rm -f" $$files ")"; \
	cd "$(DESTDIR)$(perlmoddir)" && rm -f $$files

mostlyclean-libtool:
	-rm -f *.lo

clean-libtool:
	-rm -rf .libs _libs
tags: TAGS
TAGS:

ctags: CTAGS
CTAGS:


check-TESTS: $(TESTS)
	@failed=0; all=0; xfail=0; xpass=0; skip=0; \
	srcdir=$(srcdir); export srcdir; \
	list=' $(TESTS) '; \
	$(am__tty_colors); \
	if test -n "$$list"; then \
	  for tst in $$list; do \
	    if test -f ./$$tst; then dir=./; \
	    elif test -f $$tst; then dir=; \
	    else dir="$(srcdir)/"; fi; \
	    if $(TESTS_ENVIRONMENT) $${dir}$$tst; then \
	      all=`expr $$all + 1`; \
	      case " $(XFAIL_TESTS) " in \
	      *[\ \	]$$tst[\ \	]*) \
		xpass=`expr $$xpass + 1`; \
		failed=`expr $$failed + 1`; \
		col=$$red; res=XPASS; \
	      ;; \
	      *) \
		col=$$grn; res=PASS; \
	      ;; \
	      esac; \
	    elif test $$? -ne 77; then \
	      all=`expr $$all + 1`; \
	      case " $(XFAIL_TESTS) " in \
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		xfail=`expr $$xfail + 1`; \
		col=$$lgn; res=XFAIL; \
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		failed=`expr $$failed + 1`; \
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	      ;; \
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	    else \
	      skip=`expr $$skip + 1`; \
	      col=$$blu; res=SKIP; \
	    fi; \
	    echo "$${col}$$res$${std}: $$tst"; \
	  done; \
	  if test "$$all" -eq 1; then \
	    tests="test"; \
	    All=""; \
	  else \
	    tests="tests"; \
	    All="All "; \
	  fi; \
	  if test "$$failed" -eq 0; then \
	    if test "$$xfail" -eq 0; then \
	      banner="$$All$$all $$tests passed"; \
	    else \
	      if test "$$xfail" -eq 1; then failures=failure; else failures=failures; fi; \
	      banner="$$All$$all $$tests behaved as expected ($$xfail expected $$failures)"; \
	    fi; \
	  else \
	    if test "$$xpass" -eq 0; then \
	      banner="$$failed of $$all $$tests failed"; \
	    else \
	      if test "$$xpass" -eq 1; then passes=pass; else passes=passes; fi; \
	      banner="$$failed of $$all $$tests did not behave as expected ($$xpass unexpected $$passes)"; \
	    fi; \
	  fi; \
	  dashes="$$banner"; \
	  skipped=""; \
	  if test "$$skip" -ne 0; then \
	    if test "$$skip" -eq 1; then \
	      skipped="($$skip test was not run)"; \
	    else \
	      skipped="($$skip tests were not run)"; \
	    fi; \
	    test `echo "$$skipped" | wc -c` -le `echo "$$banner" | wc -c` || \
	      dashes="$$skipped"; \
	  fi; \
	  report=""; \
	  if test "$$failed" -ne 0 && test -n "$(PACKAGE_BUGREPORT)"; then \
	    report="Please report to $(PACKAGE_BUGREPORT)"; \
	    test `echo "$$report" | wc -c` -le `echo "$$banner" | wc -c` || \
	      dashes="$$report"; \
	  fi; \
	  dashes=`echo "$$dashes" | sed s/./=/g`; \
	  if test "$$failed" -eq 0; then \
	    echo "$$grn$$dashes"; \
	  else \
	    echo "$$red$$dashes"; \
	  fi; \
	  echo "$$banner"; \
	  test -z "$$skipped" || echo "$$skipped"; \
	  test -z "$$report" || echo "$$report"; \
	  echo "$$dashes$$std"; \
	  test "$$failed" -eq 0; \
	else :; fi

distdir: $(DISTFILES)
	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
	list='$(DISTFILES)'; \
	  dist_files=`for file in $$list; do echo $$file; done | \
	  sed -e "s|^$$srcdirstrip/||;t" \
	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
	case $$dist_files in \
	  */*) $(MKDIR_P) `echo "$$dist_files" | \
			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
			   sort -u` ;; \
	esac; \
	for file in $$dist_files; do \
	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
	  if test -d $$d/$$file; then \
	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
	    if test -d "$(distdir)/$$file"; then \
	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
	    fi; \
	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
	    fi; \
	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
	  else \
	    test -f "$(distdir)/$$file" \
	    || cp -p $$d/$$file "$(distdir)/$$file" \
	    || exit 1; \
	  fi; \
	done
	$(MAKE) $(AM_MAKEFLAGS) \
	  top_distdir="$(top_distdir)" distdir="$(distdir)" \
	  dist-hook
check-am: all-am
	$(MAKE) $(AM_MAKEFLAGS) check-TESTS
check: check-am
all-am: Makefile $(SCRIPTS)
installdirs:
	for dir in "$(DESTDIR)$(bindir)" "$(DESTDIR)$(perlmoddir)"; do \
	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
	done
install: install-am
install-exec: install-exec-am
install-data: install-data-am
uninstall: uninstall-am

install-am: all-am
	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am

installcheck: installcheck-am
install-strip:
	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
	  `test -z '$(STRIP)' || \
	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
mostlyclean-generic:

clean-generic:
	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)

distclean-generic:
	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)

maintainer-clean-generic:
	@echo "This command is intended for maintainers to use"
	@echo "it deletes files that may require special tools to rebuild."
clean: clean-am

clean-am: clean-generic clean-libtool mostlyclean-am

distclean: distclean-am
	-rm -f Makefile
distclean-am: clean-am distclean-generic

dvi: dvi-am

dvi-am:

html: html-am

html-am:

info: info-am

info-am:

install-data-am: install-perlmodSCRIPTS

install-dvi: install-dvi-am

install-dvi-am:

install-exec-am: install-binSCRIPTS

install-html: install-html-am

install-html-am:

install-info: install-info-am

install-info-am:

install-man:

install-pdf: install-pdf-am

install-pdf-am:

install-ps: install-ps-am

install-ps-am:

installcheck-am:

maintainer-clean: maintainer-clean-am
	-rm -f Makefile
maintainer-clean-am: distclean-am maintainer-clean-generic

mostlyclean: mostlyclean-am

mostlyclean-am: mostlyclean-generic mostlyclean-libtool

pdf: pdf-am

pdf-am:

ps: ps-am

ps-am:

uninstall-am: uninstall-binSCRIPTS uninstall-perlmodSCRIPTS

.MAKE: check-am install-am install-strip

.PHONY: all all-am check check-TESTS check-am clean clean-generic \
	clean-libtool dist-hook distclean distclean-generic \
	distclean-libtool distdir dvi dvi-am html html-am info info-am \
	install install-am install-binSCRIPTS install-data \
	install-data-am install-dvi install-dvi-am install-exec \
	install-exec-am install-html install-html-am install-info \
	install-info-am install-man install-pdf install-pdf-am \
	install-perlmodSCRIPTS install-ps install-ps-am install-strip \
	installcheck installcheck-am installdirs maintainer-clean \
	maintainer-clean-generic mostlyclean mostlyclean-generic \
	mostlyclean-libtool pdf pdf-am ps ps-am uninstall uninstall-am \
	uninstall-binSCRIPTS uninstall-perlmodSCRIPTS

@PARALLEL_IS_LAM_TRUE@@PARALLEL_TRUE@runcheck_p: runcheck_p.sh.in Makefile
@PARALLEL_IS_LAM_TRUE@@PARALLEL_TRUE@	sed -e "s%@mpirun@%$(top_srcdir)/scripts/lrun -n %" $< > runcheck_p; \
@PARALLEL_IS_LAM_TRUE@@PARALLEL_TRUE@  chmod +x runcheck_p;
@PARALLEL_IS_LAM_FALSE@@PARALLEL_TRUE@runcheck_p: runcheck_p.sh.in Makefile
@PARALLEL_IS_LAM_FALSE@@PARALLEL_TRUE@	sed -e "s%@mpirun@%$(MPI_CMD) %" $< > runcheck_p; \
@PARALLEL_IS_LAM_FALSE@@PARALLEL_TRUE@  chmod +x runcheck_p

# Describe dependencies and build instructions for scripts.
# (substitute in local path to Perl).

# input files with unusual build names
convert2html.pl: convert2html.pl.in
	$(SED) $(SEDSPEC) $< > $@; \
	chmod +x $@
MemeWebUtils.pm: MemeWebUtils.pm.in Makefile
	$(SED) $(SEDSPEC) $< > $@

# need these to allow use as a Python library or for command line
fasta-hamming-enrich.py: fasta-hamming-enrich
	cp fasta-hamming-enrich fasta-hamming-enrich.py
fasta-dinucleotide-shuffle.py: fasta-dinucleotide-shuffle
	cp fasta-dinucleotide-shuffle fasta-dinucleotide-shuffle.py

# csh input files
%: %.csh.in
	$(SED) $(SEDSPEC) $< > $@; \
  chmod +x $@

# perl input files
%: %.pl.in
	$(SED) $(SEDSPEC) $< > $@; \
  chmod +x $@

# python input files
%: %.py.in sequence.py hypergeometric.py ../ARCHIVE_DATE ../ARCHIVE_REVISION
	$(SED) $(SEDSPEC) $< > $@; \
  chmod +x $@

# If .svnignore file doesn't exist
# create an empty one
.svnignore:
	if [ -e .svn ] ; then touch .svnignore ; fi

# Update SVN svn:ignore property
# If .svnignore exists and longer then 0 bytes.
.svnignore.old:.svnignore
	if [ -e .svn ] ; \
  then \
    if [ -s .svnignore ] ; \
    then \
      svn propset svn:ignore -F .svnignore .  ; \
      cp .svnignore .svnignore.old; \
    fi \
  fi

dist-hook:
	rm -f $(distdir)/metatest
	rm -f $(distdir)/runcheck_p

# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
.NOEXPORT:
