# Makefile.in generated by automake 1.11.3 from Makefile.am.
# distribution/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, 2010, 2011 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)/mira
pkgincludedir = $(includedir)/mira
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NORMAL_UNINSTALL = :
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CONFIG_CLEAN_VPATH_FILES =
SOURCES =
DIST_SOURCES =
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = ${SHELL} /home/bach/work/assembly/mira.git/missing --run aclocal-1.11
AMTAR = $${TAR-tar}
AR = ar
AUTOCONF = ${SHELL} /home/bach/work/assembly/mira.git/missing --run autoconf
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BOOST_FILESYSTEM_LIB = -lboost_filesystem
BOOST_IOSTREAMS_LIB = -lboost_iostreams
BOOST_LDFLAGS = -L/opt/biosw/lib
BOOST_REGEX_LIB = -lboost_regex
BOOST_SYSTEM_LIB = -lboost_system
BOOST_THREAD_LIB = -lboost_thread
BUNDLETARGET = darwin
CC = gcc
CCDEPMODE = depmode=gcc3
CFLAGS =   -I/opt/biosw/include -g -W -Wstrict-prototypes -fno-strict-aliasing -Wextra -ansi -Wbad-function-cast -Wcast-align -Wcast-qual -Wchar-subscripts -Wmissing-prototypes -Wnested-externs -Wpointer-arith -Wredundant-decls -Wshadow -Wstrict-prototypes -Wwrite-strings -Wformat -Wimplicit -Wmissing-braces -Wparentheses -Wswitch -Wswitch-default -Wswitch-enum -Wunused -Wfloat-equal -Wendif-labels -Wconversion -Wdisabled-optimization -Wsequence-point -Werror=unused-value -Werror=uninitialized -Werror=return-type 
CPP = gcc -E
CPPFLAGS = 
CXX = g++
CXXCPP = g++ -E
CXXDEPMODE = depmode=gcc3
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CYGPATH_W = echo
DEFS = -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.5\" -DPACKAGE_STRING=\"mira\ 4.9.5\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.5\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1
DEPDIR = .deps
DLLTOOL = false
DSYMUTIL = 
DUMPBIN = 
ECHO_C = 
ECHO_N = echo -n
ECHO_T = 
EGREP = /bin/grep -E
EXEEXT = 
EXPAT_CFLAGS = -I/opt/biosw/include
EXPAT_LDFLAGS = -L/opt/biosw/lib
EXPAT_LIBS = -lexpat
EXPAT_VERSION = 
FGREP = /bin/grep -F
FLEX = yes
FLEXPP = yes
GREP = /bin/grep
HAVE_XXD = yes
INSTALL = /usr/bin/install -c
INSTALL_DATA = ${INSTALL} -m 644
INSTALL_PROGRAM = ${INSTALL}
INSTALL_SCRIPT = ${INSTALL}
INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
LD = /usr/bin/ld -m elf_x86_64
LDFLAGS =  -L/opt/biosw/lib -L/opt/biosw/lib
LEX = flex
LEXLIB = -lfl
LEX_OUTPUT_ROOT = lex.yy
LIBOBJS = 
LIBS =  -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz
LIBTOOL = $(SHELL) $(top_builddir)/libtool
LIPO = 
LN_S = ln -s
LTLIBOBJS = 
MAKEINFO = ${SHELL} /home/bach/work/assembly/mira.git/missing --run makeinfo
MANIFEST_TOOL = :
MIRASTATIC = static
MKDIR_P = /bin/mkdir -p
NM = /usr/bin/nm -B
NMEDIT = 
OBJDUMP = objdump
OBJEXT = o
OTOOL = 
OTOOL64 = 
PACKAGE = mira
PACKAGE_BUGREPORT = 
PACKAGE_NAME = mira
PACKAGE_STRING = mira 4.9.5
PACKAGE_TARNAME = mira
PACKAGE_URL = 
PACKAGE_VERSION = 4.9.5
PATH_SEPARATOR = :
RANLIB = ranlib
SED = /bin/sed
SET_MAKE = 
SHELL = /bin/bash
STRIP = strip
VERSION = 4.9.5
abs_builddir = /home/bach/work/assembly/mira.git/distribution
abs_srcdir = /home/bach/work/assembly/mira.git/distribution
abs_top_builddir = /home/bach/work/assembly/mira.git
abs_top_srcdir = /home/bach/work/assembly/mira.git
ac_ct_AR = ar
ac_ct_CC = 
ac_ct_CXX = g++
ac_ct_DUMPBIN = 
am__include = include
am__leading_dot = .
am__quote = 
am__tar = tar --format=ustar -chf - "$$tardir"
am__untar = tar -xf -
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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} /home/bach/work/assembly/mira.git/install-sh
libdir = ${exec_prefix}/lib
libexecdir = ${exec_prefix}/libexec
localedir = ${datarootdir}/locale
localstatedir = ${prefix}/var
mandir = ${datarootdir}/man
mkdir_p = /bin/mkdir -p
oldincludedir = /usr/include
pdfdir = ${docdir}
prefix = /usr/local
program_transform_name = s,x,x,
psdir = ${docdir}
sbindir = ${exec_prefix}/sbin
sharedstatedir = ${prefix}/com
srcdir = .
sysconfdir = ${prefix}/etc
target_alias = 
top_build_prefix = ../
top_builddir = ..
top_srcdir = ..
GITSHORT = `$(top_srcdir)/build-aux/git-version-gen isshort $(top_srcdir)/.tarball-version`
MIRAVERSION = ${GITSHORT}_${build_os}_${BITPACKAGE}_${MIRASTATIC}
MIRADIR = ${PACKAGE_TARNAME}_${MIRAVERSION}
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	      exit 1;; \
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	$(am__cd) $(top_srcdir) && \
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Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
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$(top_srcdir)/configure:  $(am__configure_deps)
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$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
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$(am__aclocal_m4_deps):

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

ctags: CTAGS
CTAGS:


distdir: $(DISTFILES)
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all-am: Makefile
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install-exec: install-exec-am
install-data: install-data-am
uninstall: uninstall-am

install-am: all-am
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installcheck: installcheck-am
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clean-generic:

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

distclean: distclean-am
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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-dvi: install-dvi-am

install-dvi-am:

install-exec-am:

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
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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:

.MAKE: install-am install-strip

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3rdparty:
	rm -rf 3rdparty
	cp -R -L ../src/3rdparty .
	tar cvjf mira_3rdparty_`date +%d-%m-%Y`.tar.bz2 3rdparty

libbundle-nobundle:
	@echo "Do not need to bundle on this platform"

libbundle-darwin:
	@echo "Using Macdylibbundler to create OSX compatible dylib references"
	(cd ${MIRADIR}; dylibbundler -b -od -d lib -p @executable_path/../lib/ -x bin/mira; cd ..)

copybin:
	@echo "Making distribution for ${BITPACKAGE}"
	-rm -rf ${MIRADIR} *.tar *.gz
	mkdir ${MIRADIR}
	mkdir ${MIRADIR}/bin
	cp ../src/progs/mira ${MIRADIR}/bin
	ln -s -f mira ${MIRADIR}/bin/mirabait
	ln -s -f mira ${MIRADIR}/bin/miraconvert
	ln -s -f mira ${MIRADIR}/bin/miramem
#	ln -s -f mira ${MIRADIR}/bin/miraSearchESTSNPs
#	ln -s -f mira ${MIRADIR}/bin/miraclip
	mkdir ${MIRADIR}/scripts
	cp ../src/scripts/fixACE4consed.tcl ${MIRADIR}/scripts
	cp ../src/scripts/fasta2frag.tcl ${MIRADIR}/scripts

copydocs:
	mkdir ${MIRADIR}/docs
	cp -R -L ../doc/docbook/Defi*.html ${MIRADIR}/docs
	( cd ${MIRADIR}/docs; ln -s DefinitiveGuideToMIRA.html index.html)
	cp -R -L ../doc/docbook/*.pdf ${MIRADIR}/docs
	cp -R -L ../doc/docbook/bookfigures ${MIRADIR}/docs
	cp -R -L ../doc/docbook/images ${MIRADIR}/docs
	cp -R -L ../doc/docbook/doccss ${MIRADIR}/docs

distribin: copybin libbundle-${BUNDLETARGET}
	strip ${MIRADIR}/bin/*
	tar cvjf ${PACKAGE_TARNAME}_binonly_${MIRAVERSION}.tar.bz2 ${MIRADIR}

distridbg: copybin libbundle-${BUNDLETARGET}
	rm -rf ${MIRADIR}/scripts
	tar cvjf ${PACKAGE_TARNAME}_dbgonly_${MIRAVERSION}.tar.bz2 ${MIRADIR}

distrib: copybin libbundle-${BUNDLETARGET} copydocs
	cp ../THANKS ${MIRADIR}
	cp README ${MIRADIR}
	cp LICENCE ${MIRADIR}
	cp -R -L ../src/support ${MIRADIR}
	rm -rf ${MIRADIR}/support/Makefile*
#	cp ../src/mira/demoparam.prm ${MIRADIR}/paramtemplates.par
	cp ../src/mira/CHANGES.txt ${MIRADIR}
	cp ../src/mira/CHANGES_old.txt ${MIRADIR}
#	cp -R -L ../minidemo ${MIRADIR}
#	( cd ${MIRADIR}/minidemo/demo1; lndir ../data/scf; lndir ../data/exp_set1; ls -1 *exp >mira_in.fofn; rm fofn)
	tar cvjf ${PACKAGE_TARNAME}_${MIRAVERSION}_fullsymbols.tar.bz2 ${MIRADIR}
	strip ${MIRADIR}/bin/*
	tar cvjf ${PACKAGE_TARNAME}_${MIRAVERSION}.tar.bz2 ${MIRADIR}

clean:
	rm -rf mira_*
	rm -rf 3rdparty*

# 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:
