# Makefile.in generated by automake 1.11.1 from Makefile.am. # src/Makefile. Generated from Makefile.in by configure. # 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. pkgdatadir = $(datadir)/meme pkgincludedir = $(includedir)/meme pkglibdir = $(libdir)/meme pkglibexecdir = $(libexecdir)/meme 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 = : 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AMTAR = ${SHELL} /data/MEME/meme_4.7.0/config/missing --run tar ANT = /usr/bin/ant AR = ar AUTOCONF = ${SHELL} /data/MEME/meme_4.7.0/config/missing --run autoconf AUTOHEADER = ${SHELL} /data/MEME/meme_4.7.0/config/missing --run autoheader AUTOMAKE = ${SHELL} /data/MEME/meme_4.7.0/config/missing --run automake-1.11 AWK = gawk BLOCKS_URL = http://blocks.fhcrc.org/blocks-bin/process_blocks.pl CC = gcc CCDEPMODE = depmode=gcc3 CFLAGS = -Wall -Wno-unused -DUNIX -D__USE_FIXED_PROTOTYPES__ -O3 CONTACT = @mus CONVERT = /usr/bin/convert CPP = gcc -E CPPFLAGS = CYGPATH_W = echo DEBUG_FLAGS = DEFS = -DHAVE_CONFIG_H DEPDIR = .deps DOT = /usr/bin/dot DSYMUTIL = DUMPBIN = ECHO_C = ECHO_N = -n ECHO_T = EGREP = /bin/grep -E EXEEXT = FGREP = /bin/grep -F GHOSTSCRIPT = /usr/bin/gs GOSERVER_URL = http://amigo.geneontology.org/cgi-bin/amigo/ GREP = /bin/grep HAVE_ELINKS = no HOSTNAME = mus INSTALL = /usr/bin/install -c INSTALL_DATA = ${INSTALL} -m 644 INSTALL_PROGRAM = ${INSTALL} INSTALL_SCRIPT = ${INSTALL} INSTALL_STRIP_PROGRAM = $(install_sh) -c -s LAMBIN = LD = /usr/bin/ld -m elf_x86_64 LDFLAGS = LIBEXSLT_CFLAGS = -I${top_srcdir}/src/libexslt LIBEXSLT_LIBS = ${top_builddir}/src/libexslt/libexslt.la LIBOBJS = LIBS = -lmpi -lm LIBTOOL = $(SHELL) $(top_builddir)/libtool LIBXML2_CFLAGS = -I${top_srcdir}/src/libxml2/include LIBXML2_LIBS = ${top_builddir}/src/libxml2/libxml2.la LIBXSLT_CFLAGS = -I${top_srcdir}/src/ LIBXSLT_LIBS = ${top_builddir}/src/libxslt/libxslt.la LIPO = LN_S = ln -s LTLIBOBJS = MACHID = linux MAIL = /usr/bin/mail MAKEINFO = ${SHELL} /data/MEME/meme_4.7.0/config/missing --run makeinfo MAST_PORT = MAXTIME = 7200 MEME_DB = ${prefix}/db MEME_DIRECTORY = ${prefix} MEME_LOGS = ${prefix}/LOGS MEME_PORT = MEME_TEMP = MKDIR_P = /bin/mkdir -p MPICC = /usr/bin/mpicc MPIFLAGS = -DPARALLEL MPIINC = -DMPI -I/usr/include MPILIBDIR = /usr/lib MPITYPE = mpich MPI_CMD = /usr/bin/mpirun -np NM = /usr/bin/nm -B NMEDIT = OBJDUMP = objdump OBJEXT = o OPAL_URL = no OPAL_XML = no OPT_FLAGS = -O3 OTOOL = OTOOL64 = PACKAGE = meme PACKAGE_BUGREPORT = PACKAGE_NAME = meme PACKAGE_STRING = meme 4.7.0 PACKAGE_TARNAME = meme PACKAGE_URL = PACKAGE_VERSION = 4.7.0 PATH_SEPARATOR = : PERL = /usr/local/bin/perl PYTHON = /usr/bin/python RANLIB = ranlib SED = /bin/sed SENDMAIL = /usr/sbin/sendmail SET_MAKE = SHELL = /bin/bash STRIP = strip URL = http://meme.nbcr.net/meme VERSION = 4.7.0 WEBDIR = ${prefix}/web WEBSERVICE = XML2_CONFIG = XSLT_CONFIG = abs_builddir = /data/MEME/meme_4.7.0/src abs_srcdir = /data/MEME/meme_4.7.0/src abs_top_builddir = /data/MEME/meme_4.7.0 abs_top_srcdir = /data/MEME/meme_4.7.0 ac_ct_CC = gcc ac_ct_DUMPBIN = am__include = include am__leading_dot = . am__quote = am__tar = tar --format=posix -chf - "$$tardir" am__untar = tar -xf - bindir = ${exec_prefix}/bin build = x86_64-unknown-linux-gnu build_alias = build_cpu = x86_64 build_os = linux-gnu build_vendor = unknown builddir = . datadir = ${datarootdir} datarootdir = ${prefix}/share docdir = ${datarootdir}/doc/${PACKAGE_TARNAME} dvidir = ${docdir} exec_prefix = ${prefix} host = x86_64-unknown-linux-gnu host_alias = host_cpu = x86_64 host_os = linux-gnu host_vendor = unknown htmldir = ${docdir} includedir = ${prefix}/include infodir = ${datarootdir}/info install_sh = ${SHELL} /data/MEME/meme_4.7.0/config/install-sh libdir = ${exec_prefix}/lib libexecdir = ${exec_prefix}/libexec localedir = ${datarootdir}/locale localstatedir = ${prefix}/var lt_ECHO = echo mandir = ${datarootdir}/man mkdir_p = /bin/mkdir -p oldincludedir = /usr/include pdfdir = ${docdir} prefix = /home/rmott/meme program_transform_name = s,x,x, psdir = ${docdir} sbindir = ${exec_prefix}/sbin sharedstatedir = ${prefix}/com srcdir = . sysconfdir = ${prefix}/etc target_alias = top_build_prefix = ../ top_builddir = .. top_srcdir = .. #PARALLEL_DIR = ##################################################################### # # $Id: Makefile.am 6048 2011-09-28 07:09:50Z james_johnson $ # ##################################################################### # Note: # # To change compiler options at build time set the CFLAGS parameter # on the make command line. For example, to turn on debugging symbols, # turn off optimization and turn on the DEBUG preprocessor definition # the command line would be: # # make CFLAGS=" -ggdb -O0 -DDEBUG" # ##################################################################### PARALLEL_DIR = parallel SUBDIRS = filters libxml2 libxslt libexslt . $(PARALLEL_DIR) BUILT_SOURCES = dir.h projrel.h PROGS = \ alphtype \ ama \ ame \ beadstring \ ceqlogo \ centrimo \ clustalw-io \ clustalw2fasta \ clustalw2phylip \ compute-prior-dist \ compute-uniform-priors \ draw-mhmm \ fasta-io \ fimo \ fitevd \ gendb \ getsize \ glam2 \ glam2format \ glam2mask \ glam2scan \ gomo \ gomo_highlight \ llr \ log-hmm \ mast \ mast2txt \ mcast \ meme.bin \ meme-xml-html \ meme2images \ mhmm \ mhmm-io \ mhmme \ mhmms \ mhmmscan \ motiph \ pmp_bf \ readseq \ shadow \ spamo \ tomtom \ tree \ qvalue \ ranksum_test \ reconcile-tree-alignment \ reduce-alignment \ remove-alignment-gaps \ xsltproc_lite noinst_LTLIBRARIES = libcommon.la # Build the source common to all the binaries into a library libcommon_la_CFLAGS = \ -fno-strict-aliasing \ $(AM_CFLAGS) \ $(LIBXML2_CFLAGS) \ $(LIBXSLT_CFLAGS) \ $(LIBEXSLT_CFLAGS) libcommon_la_LIBADD = \ $(LIBXML2_LIBS) \ $(LIBXSLT_LIBS) \ $(LIBEXSLT_LIBS) \ -lm libcommon_la_SOURCES = \ alignment.c \ alphabet.c \ array.c \ array-list.c \ background.c \ binary-search.c \ build-hmm.c \ buffer.c \ ceqlogo.c \ cisml.c \ clustalw-io.c \ dp.c \ dreme-sax.c \ eps2png.c \ empirical-qvalue.c \ evomodel.c \ evomodel_with_loss.c \ fasta-io.c \ fisher_exact.c \ fisher_exact.h \ fitevd.c \ gendb.c \ hash_alph.c \ hash_table.c \ heap.c \ html-data.c \ io.c \ karlin.c \ linked-list.c \ log-hmm.c \ logodds.c \ mast-util.c \ match.c \ matrix.c \ meme-sax.c \ metameme.c \ mhmm.c \ mhmms.c \ mhmm-state.c \ motif-in.c \ motif-in-common.c \ motif-in-dreme-xml.c \ motif-in-meme-html.c \ motif-in-meme-text.c \ motif-in-meme-xml.c \ motif.c \ motif_regexp.c \ motifs.c \ motiph-scoring.c \ object-list.c \ order.c \ data-block.c \ data-block-reader.c \ prior-reader-from-psp.c \ prior-dist.c \ pssm.c \ pssm-distr.c \ qvalue.c \ ranksum_test.c \ ranksum_test.h \ rdb-matrix.c \ read-mhmm.c \ read_sequence.c \ red-black-tree.c \ regex-utils.c \ regress.c \ reservoir.c \ sax-parser-utils.c \ scanned-sequence.c \ scored-sites.c \ seq.c \ seq-reader-from-fasta.c \ simple-getopt.c \ spearman-rank-correlation.c \ spearman-rank-correlation.h \ string-builder.c \ string-list.c \ string-match.c \ subst-matrix.c \ substmatrix-table.c \ tree.c \ utils.c \ write-mhmm.c \ xml-out.c \ xml-util.c alphtype_CFLAGS = $(AM_CFLAGS) alphtype_LDADD = libcommon.la alphtype_SOURCES = alphtype.c # Describe the source files and build options for each executable ama_CFLAGS = $(AM_CFLAGS) $(LIBXML2_CFLAGS) $(LIBXSLT_CFLAGS) $(OPENMP_CFLAGS) ama_LDADD = libcommon.la $(LIBXML2_LIBS) $(LIBXSLT_LIBS) ama_SOURCES = \ ama.c \ ama_scan.c ame_CFLAGS = -DMAIN $(AM_CFLAGS) $(LIBXML2_CFLAGS) ame_SOURCES = ame.c ame_LDADD = libcommon.la $(LIBXML2_LIBS) $(LIBXSLT_LIBS) -lm beadstring_CFLAGS = $(AM_CFLAGS) $(LIBXML2_CFLAGS) $(LIBXSLT_CFLAGS) beadstring_LDADD = libcommon.la $(LIBXML2_LIBS) $(LIBXSLT_LIBS) beadstring_SOURCES = beadstring.c centrimo_CFLAGS = $(AM_CFLAGS) $(LIBXML2_CFLAGS) $(LIBXSLT_CFLAGS) centrimo_LDADD = libcommon.la $(LIBXML2_LIBS) $(LIBXSLT_LIBS) centrimo_SOURCES = centrimo.c ceqlogo_CFLAGS = -DCL_MAIN $(AM_CFLAGS) $(LIBXML2_CFLAGS) $(LIBXSLT_CFLAGS) ceqlogo_LDADD = libcommon.la $(LIBXML2_LIBS) $(LIBXSLT_LIBS) ceqlogo_SOURCES = ceqlogo.c clustalw_io_CFLAGS = -DMAIN $(AM_CFLAGS) clustalw_io_LDADD = libcommon.la clustalw_io_SOURCES = clustalw-io.c clustalw2fasta_CFLAGS = $(AM_CFLAGS) clustalw2fasta_LDADD = libcommon.la clustalw2fasta_SOURCES = clustalw2fasta.c clustalw2phylip_CFLAGS = $(AM_CFLAGS) clustalw2phylip_LDADD = libcommon.la clustalw2phylip_SOURCES = clustalw2phylip.c compute_prior_dist_CFLAGS = $(AM_CFLAGS) compute_prior_dist_LDADD = libcommon.la compute_prior_dist_SOURCES = compute-prior-dist.c compute_uniform_priors_CFLAGS = $(AM_CFLAGS) compute_uniform_priors_LDADD = libcommon.la compute_uniform_priors_SOURCES = compute-uniform-priors.c draw_mhmm_CFLAGS = -DMAIN $(AM_CFLAGS) $(LIBXML2_CFLAGS) $(LIBXSLT_CFLAGS) draw_mhmm_LDADD = libcommon.la draw_mhmm_SOURCES = \ draw-mhmm.c \ read-mhmm.c fasta_io_CFLAGS = -DMAIN $(AM_CFLAGS) fasta_io_LDADD = libcommon.la fasta_io_SOURCES = fasta-io.c fimo_CFLAGS = $(AM_CFLAGS) $(LIBXML2_CFLAGS) $(LIBXSLT_CFLAGS) fimo_LDADD = libcommon.la $(LIBXML2_LIBS) $(LIBXSLT_LIBS) fimo_SOURCES = fimo.c fitevd_CFLAGS = -DMAIN $(AM_CFLAGS) fitevd_LDADD = libcommon.la fitevd_SOURCES = fitevd.c gendb_CFLAGS = -DMAIN $(AM_CFLAGS) gendb_LDADD = libcommon.la gendb_SOURCES = gendb.c getsisze_CFLAGS = $(AM_CFLAGS) getsize_LDADD = libcommon.la getsize_SOURCES = getsize.c glam2_CFLAGS = $(AM_CFLAGS) glam2_LDADD = libcommon.la glam2_SOURCES = \ glam2_alphabet.c \ glam2_args.c \ glam2_column_sample.c \ glam2_dirichlet.c \ glam2_dna_prior.c \ glam2_fasta.c \ glam2_glam2.c \ glam2_glam2_aln.c \ glam2_init.c \ glam2_output.c \ glam2_recode3_20comp.c \ glam2_site_sample.c \ glam2_util.c glam2scan_CFLAGS = $(AM_CFLAGS) glam2scan_LDADD = libcommon.la glam2scan_SOURCES = \ glam2_alignment.c \ glam2_alphabet.c \ glam2_dna_prior.c \ glam2_fasta.c \ glam2_dirichlet.c \ glam2_heap.c \ glam2_motif.c \ glam2_scan.c \ glam2_scan_args.c \ glam2_scan_init.c \ glam2_scan_output.c \ glam2_recode3_20comp.c \ glam2_util.c glam2format_CFLAGS = $(AM_CFLAGS) glam2format_LDADD = libcommon.la glam2format_SOURCES = \ glam2_glam2format.c \ glam2_alignment.c \ glam2_fasta.c \ glam2_util.c glam2mask_CFLAGS = $(AM_CFLAGS) glam2mask_LDADD = libcommon.la glam2mask_SOURCES = \ glam2_glam2mask.c \ glam2_alignment.c \ glam2_fasta.c \ glam2_util.c gomo_CFLAGS = $(AM_CFLAGS) $(LIBXML2_CFLAGS) $(LIBXSLT_CFLAGS) $(OPENMP_CFLAGS) gomo_LDADD = libcommon.la $(LIBXML2_LIBS) $(LIBXSLT_LIBS) gomo_SOURCES = \ gomo.c \ gomo_highlight.c \ merger.c \ ranksum_test.c \ read_csv.c gomo_highlight_CFLAGS = -DMAIN $(AM_CFLAGS) gomo_highlight_LDADD = libcommon.la gomo_highlight_SOURCES = gomo_highlight.c log_hmm_CFLAGS = -DMAIN $(AM_CFLAGS) $(LIBXML2_CFLAGS) log_hmm_LDADD = libcommon.la $(LIBXML2_LIBS) $(LIBXSLT_LIBS) log_hmm_SOURCES = log-hmm.c mast_CFLAGS = $(AM_CFLAGS) $(LIBXML2_CFLAGS) $(LIBXSLT_CFLAGS) mast_LDADD = libcommon.la $(LIBXML2_LIBS) $(LIBXSLT_LIBS) mast_SOURCES = \ diagram.c \ mast.c mast2txt_CFLAGS = $(AM_CFLAGS) $(LIBXML2_CFLAGS) $(LIBXSLT_CFLAGS) mast2txt_LDADD = libcommon.la $(LIBXML2_LIBS) $(LIBXSLT_LIBS) mast2txt_SOURCES = \ mast2txt.c mcast_CFLAGS = $(AM_CFLAGS) $(LIBXML2_CFLAGS) $(LIBXSLT_CFLAGS) mcast_LDADD = libcommon.la $(LIBXML2_LIBS) $(LIBXSLT_LIBS) mcast_SOURCES = mcast.c meme_bin_CFLAGS = \ $(AM_CFLAGS) \ $(LIBXML2_CFLAGS) \ $(LIBXSLT_CFLAGS) \ $(LIBEXSLT_CFLAGS) meme_bin_LDADD = \ libcommon.la \ $(LIBXML2_LIBS) \ $(LIBXSLT_LIBS) \ $(LIBEXSLT_LIBS) meme_bin_SOURCES = \ banner.c \ branching_search.c \ calculate_p_y.c \ discretize.c \ display.c \ dpalign.c \ em.c \ init.c \ justlike.c \ likelihood.c \ llr.c \ logs.c \ meme.c \ meme-print-html.c \ meme_util.c \ message.c \ mp.c \ oops.c \ partition.c \ prior.c \ psp.c \ read_seq_file.c \ seed.c \ seed_diffs.c \ seq2theta.c \ sp_matrix.c \ starts.c \ subseq7.c \ tcm.c \ verbosity.c meme_xml_html_CFLAGS = ${meme_bin_CFLAGS} meme_xml_html_LDADD = $(LIBXML2_LIBS) $(LIBXSLT_LIBS) $(LIBEXSLT_LIBS) -lm meme_xml_html_SOURCES = \ meme-xml-html.c \ meme-print-html.c meme2images_CFLAGS = $(AM_CFLAGS) meme2images_LDADD = libcommon.la meme2images_SOURCES = meme2images.c mhmm_CFLAGS = -DMAIN $(AM_CFLAGS) mhmm_LDADD = libcommon.la mhmm_SOURCES = mhmm.c mhmm_io_CFLAGS = -DMAIN $(AM_CFLAGS) $(LIBXML2_CFLAGS) $(LIBXSLT_CFLAGS) mhmm_io_LDADD = libcommon.la mhmm_io_SOURCES = mhmm-io.c mhmme_CFLAGS = -DMAIN $(AM_CFLAGS) $(LIBXML2_CFLAGS) $(LIBXSLT_CFLAGS) mhmme_LDADD = libcommon.la mhmme_SOURCES = mhmme.c mhmms_CFLAGS = -DMAIN $(AM_CFLAGS) $(LIBXML2_CFLAGS) $(LIBXSLT_CFLAGS) mhmms_LDADD = libcommon.la mhmms_SOURCES = mhmms.c mhmmscan_CFLAGS = -DMAIN $(AM_CFLAGS) $(LIBXML2_CFLAGS) $(LIBXSLT_CFLAGS) mhmmscan_LDADD = libcommon.la mhmmscan_SOURCES = mhmmscan.c motiph_CFLAGS = -DMOTIPH $(AM_CFLAGS) $(LIBXML2_CFLAGS) motiph_LDADD = libcommon.la motiph_SOURCES = motiph.c pmp_bf_CFLAGS = -DMOTIPH $(AM_CFLAGS) $(LIBXML2_CFLAGS) pmp_bf_LDADD = libcommon.la pmp_bf_SOURCES = pmp_bf.c readseq_CFLAGS = $(AM_CFLAGS) readseq_SOURCES = \ readseq.c \ ureadseq.c shadow_CFLAGS = -DSHADOW $(AM_CFLAGS) $(LIBXML2_CFLAGS) shadow_LDADD = libcommon.la shadow_SOURCES = shadow.c llr_CFLAGS = -DMAIN $(AM_CFLAGS) llr_LDADD = libcommon.la llr_SOURCES = llr.c logs.c spamo_CFLAGS = $(AM_CFLAGS) $(LIBXML2_CFLAGS) $(LIBXSLT_CFLAGS) spamo_LDADD = libcommon.la $(LIBXML2_LIBS) $(LIBXSLT_LIBS) spamo_SOURCES = \ cisml-sax.c \ spamo.c \ spamo-cisml.c \ spamo-matches.c \ spamo-output.c \ spamo-scan.c tomtom_CFLAGS = -DMAIN $(AM_CFLAGS) $(LIBXML2_CFLAGS) $(LIBXSLT_CFLAGS) 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xsltproc_lite_SOURCES = xsltproc_lite.c CLEANFILES = dir.h projrel.h DISTCLEANFILES = dir.h projrel.h #all the header files EXTRA_DIST = \ aa.h \ align.h \ alignment.h \ alphabet.h \ ame.h \ ama_scan.h \ array.h \ array-list.h \ background.h \ banner.h \ beadstring.h \ beadstring-xml.h \ binary-search.h \ buffer.h \ build-hmm.h \ calculate_p_y.h \ ceqlogo.h \ cisml-dtd.h \ cisml.h \ cisml-sax.h \ clustalw-io.h \ curves.h \ diagram.h \ dir.h \ display_globals.h \ display.h \ dpalign.h \ dp.h \ dreme-sax.h \ eps2png.h \ em.h \ empirical-qvalue.h \ evomodel.h \ evomodel_with_loss.h \ fasta-io.h \ fcodon.h \ fitevd.h \ gendb.h \ general.h \ glam2_alignment.h \ glam2_alphabet.h \ glam2_args.h \ glam2_column_sample.h \ glam2_convolve.h \ glam2_dirichlet.h \ glam2_dna_prior.h \ glam2_fasta.h \ glam2_glam2_aln.h \ glam2_glam2.h \ glam2_heap.h \ glam2_init.h \ glam2_motif.h \ glam2_output.h \ glam2_recode3_20comp.h \ glam2_scan_args.h \ glam2_scan.h \ glam2_scan_init.h \ glam2_scan_output.h \ 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