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Mark Howison committed c28ad44

README update: new url for ubuntu install script

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 install-data-local:
 Agalma is developed by the [Dunn Lab](http://dunnlab.org) at Brown University.
 
-See TUTORIAL for an example of how to use Agalma with a sample dataset.
+See [TUTORIAL](https://bitbucket.org/caseywdunn/agalma/raw/master/TUTORIAL)
+for an example of how to use Agalma with a sample dataset.
 
 
 #Overview of Agalma
 * load gene predictions from other sources into the database
 * identify homologous sequences across multiple species based on nucleotide 
   sequence similarity
-* Create amino acid and protein alignments for each set of homologous sequences 
+* Create nucleotide and protein alignments for each set of homologous sequences 
   through simultaneous alignment and translation
 * Build gene trees for each set of aligned homologous sequences
 * Identify orthologs through topological analysis of the gene trees
-* Create amino acid and protein alignments for each ortholog
+* Create nucleotide and protein alignments for each ortholog
 * Construct and analyze supermatrices of orthologs to build species phylogenies
 
 Agalma is built on top of BioLite, a bioinformatics framework written in
 On Mac OS X 10.8:
 
     brew install agalma
+    agalma blastdb
 
 On Ubuntu 12.04:
 
-    wget https://raw.github.com/caseywdunn/agalma/master/install_agalma_ubuntu.sh
+    wget https://bitbucket.org/caseywdunn/agalma/raw/master/install_agalma_ubuntu.sh
     sudo sh install_agalma_ubuntu.sh
+    agalma blastdb
 
+After installing, you can try out Agalma by following the included
+[TUTORIAL](https://bitbucket.org/caseywdunn/agalma/raw/master/TUTORIAL).
 
 We have tested Agalma on OS X 10.8, Ubuntu 12.04, and CentOS 6.3. It likely 
 works on other operating systems as well, though we have not tested this.
 
-See INSTALL for more detailed instructions, system requirements, and for how to
-configure Agalma after installing it.
+See [INSTALL](https://bitbucket.org/caseywdunn/agalma/raw/master/INSTALL)
+for more detailed instructions, system requirements, and for how to configure
+Agalma after installing it.
 
 
 
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+# Copyright (C) 1996-2012 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 rm -f conftest.file
 ])
 
-# Copyright (C) 2009-2013 Free Software Foundation, Inc.
-#
-# This file 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.
-
-# AM_SILENT_RULES([DEFAULT])
-# --------------------------
-# Enable less verbose build rules; with the default set to DEFAULT
-# ("yes" being less verbose, "no" or empty being verbose).
-AC_DEFUN([AM_SILENT_RULES],
-[AC_ARG_ENABLE([silent-rules], [dnl
-AS_HELP_STRING(
-  [--enable-silent-rules],
-  [less verbose build output (undo: "make V=1")])
-AS_HELP_STRING(
-  [--disable-silent-rules],
-  [verbose build output (undo: "make V=0")])dnl
-])
-case $enable_silent_rules in @%:@ (((
-  yes) AM_DEFAULT_VERBOSITY=0;;
-   no) AM_DEFAULT_VERBOSITY=1;;
-    *) AM_DEFAULT_VERBOSITY=m4_if([$1], [yes], [0], [1]);;
-esac
-dnl
-dnl A few 'make' implementations (e.g., NonStop OS and NextStep)
-dnl do not support nested variable expansions.
-dnl See automake bug#9928 and bug#10237.
-am_make=${MAKE-make}
-AC_CACHE_CHECK([whether $am_make supports nested variables],
-   [am_cv_make_support_nested_variables],
-   [if AS_ECHO([['TRUE=$(BAR$(V))
-BAR0=false
-BAR1=true
-V=1
-am__doit:
-	@$(TRUE)
-.PHONY: am__doit']]) | $am_make -f - >/dev/null 2>&1; then
-  am_cv_make_support_nested_variables=yes
-else
-  am_cv_make_support_nested_variables=no
-fi])
-if test $am_cv_make_support_nested_variables = yes; then
-  dnl Using '$V' instead of '$(V)' breaks IRIX make.
-  AM_V='$(V)'
-  AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
-else
-  AM_V=$AM_DEFAULT_VERBOSITY
-  AM_DEFAULT_V=$AM_DEFAULT_VERBOSITY
-fi
-AC_SUBST([AM_V])dnl
-AM_SUBST_NOTMAKE([AM_V])dnl
-AC_SUBST([AM_DEFAULT_V])dnl
-AM_SUBST_NOTMAKE([AM_DEFAULT_V])dnl
-AC_SUBST([AM_DEFAULT_VERBOSITY])dnl
-AM_BACKSLASH='\'
-AC_SUBST([AM_BACKSLASH])dnl
-_AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl
-])
-
-# Copyright (C) 2001-2013 Free Software Foundation, Inc.
+# Copyright (C) 2001-2012 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
 AC_SUBST([INSTALL_STRIP_PROGRAM])])
 
-# Copyright (C) 2006-2013 Free Software Foundation, Inc.
+# Copyright (C) 2006-2012 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 
 # Check how to create a tarball.                            -*- Autoconf -*-
 
-# Copyright (C) 2004-2013 Free Software Foundation, Inc.
+# Copyright (C) 2004-2012 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,

agalma/Makefile.in

-# Makefile.in generated by automake 1.13.1 from Makefile.am.
+# Makefile.in generated by automake 1.12.4 from Makefile.am.
 # @configure_input@
 
 # Copyright (C) 1994-2012 Free Software Foundation, Inc.
 build_triplet = @build@
 host_triplet = @host@
 subdir = agalma
-DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
-	$(srcdir)/agalma.in $(pkgpython_PYTHON) \
+DIST_COMMON = $(pkgpython_PYTHON) $(srcdir)/Makefile.am \
+	$(srcdir)/Makefile.in $(srcdir)/agalma.in \
 	$(top_srcdir)/py-compile
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
 am__aclocal_m4_deps = $(top_srcdir)/m4/ac_define_dir.m4 \
   }
 am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(pkgpythondir)"
 SCRIPTS = $(nodist_bin_SCRIPTS)
-AM_V_P = $(am__v_P_@AM_V@)
-am__v_P_ = $(am__v_P_@AM_DEFAULT_V@)
-am__v_P_0 = false
-am__v_P_1 = :
-AM_V_GEN = $(am__v_GEN_@AM_V@)
-am__v_GEN_ = $(am__v_GEN_@AM_DEFAULT_V@)
-am__v_GEN_0 = @echo "  GEN     " $@;
-am__v_GEN_1 = 
-AM_V_at = $(am__v_at_@AM_V@)
-am__v_at_ = $(am__v_at_@AM_DEFAULT_V@)
-am__v_at_0 = @
-am__v_at_1 = 
 SOURCES =
 DIST_SOURCES =
 am__can_run_installinfo = \
     *) (install-info --version) >/dev/null 2>&1;; \
   esac
 am__py_compile = PYTHON=$(PYTHON) $(SHELL) $(py_compile)
-am__pep3147_tweak = \
-  sed -e 's|\.py$$||' -e 's|[^/]*$$|__pycache__/&.*.py|'
 py_compile = $(top_srcdir)/py-compile
-am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = @ACLOCAL@
 AMTAR = @AMTAR@
-AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
 AUTOCONF = @AUTOCONF@
 AUTOHEADER = @AUTOHEADER@
 AUTOMAKE = @AUTOMAKE@
 uninstall-pkgpythonPYTHON:
 	@$(NORMAL_UNINSTALL)
 	@list='$(pkgpython_PYTHON)'; test -n "$(pkgpythondir)" || list=; \
-	py_files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
-	test -n "$$py_files" || exit 0; \
+	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+	test -n "$$files" || exit 0; \
 	dir='$(DESTDIR)$(pkgpythondir)'; \
-	pyc_files=`echo "$$py_files" | sed 's|$$|c|'`; \
-	pyo_files=`echo "$$py_files" | sed 's|$$|o|'`; \
-	py_files_pep3147=`echo "$$py_files" | $(am__pep3147_tweak)`; \
-	echo "$$py_files_pep3147";\
-	pyc_files_pep3147=`echo "$$py_files_pep3147" | sed 's|$$|c|'`; \
-	pyo_files_pep3147=`echo "$$py_files_pep3147" | sed 's|$$|o|'`; \
+	filesc=`echo "$$files" | sed 's|$$|c|'`; \
+	fileso=`echo "$$files" | sed 's|$$|o|'`; \
 	st=0; \
-	for files in \
-	  "$$py_files" \
-	  "$$pyc_files" \
-	  "$$pyo_files" \
-	  "$$pyc_files_pep3147" \
-	  "$$pyo_files_pep3147" \
-	; do \
+	for files in "$$files" "$$filesc" "$$fileso"; do \
 	  $(am__uninstall_files_from_dir) || st=$$?; \
 	done; \
 	exit $$st
-tags TAGS:
+tags: TAGS
+TAGS:
 
-ctags CTAGS:
+ctags: CTAGS
+CTAGS:
 
 cscope cscopelist:
 
 
 .MAKE: install-am install-strip
 
-.PHONY: all all-am check check-am clean clean-generic cscopelist-am \
-	ctags-am distclean distclean-generic distdir dvi dvi-am html \
-	html-am info info-am install install-am 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-nodist_binSCRIPTS \
-	install-pdf install-pdf-am install-pkgpythonPYTHON install-ps \
-	install-ps-am install-strip installcheck installcheck-am \
-	installdirs maintainer-clean maintainer-clean-generic \
-	mostlyclean mostlyclean-generic pdf pdf-am ps ps-am tags-am \
-	uninstall uninstall-am uninstall-nodist_binSCRIPTS \
-	uninstall-pkgpythonPYTHON
+.PHONY: all all-am check check-am clean clean-generic distclean \
+	distclean-generic distdir dvi dvi-am html html-am info info-am \
+	install install-am 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-nodist_binSCRIPTS install-pdf install-pdf-am \
+	install-pkgpythonPYTHON install-ps install-ps-am install-strip \
+	installcheck installcheck-am installdirs maintainer-clean \
+	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
+	pdf-am ps ps-am uninstall uninstall-am \
+	uninstall-nodist_binSCRIPTS uninstall-pkgpythonPYTHON
 
 
 # Tell versions [3.59,3.63) of GNU make to not export all variables.

autom4te.cache/output.0

 build_vendor
 build_cpu
 build
-AM_BACKSLASH
-AM_DEFAULT_VERBOSITY
-AM_DEFAULT_V
-AM_V
 am__untar
 am__tar
 AMTAR
 ac_subst_files=''
 ac_user_opts='
 enable_option_checking
-enable_silent_rules
 '
       ac_precious_vars='build_alias
 host_alias
    esac
   cat <<\_ACEOF
 
-Optional Features:
-  --disable-option-checking  ignore unrecognized --enable/--with options
-  --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no)
-  --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]
-  --enable-silent-rules   less verbose build output (undo: "make V=1")
-  --disable-silent-rules  verbose build output (undo: "make V=0")
-
 Some influential environment variables:
   PYTHON      the Python interpreter
 
 
 
 
-am__api_version='1.13'
+am__api_version='1.12'
 
 ac_aux_dir=
 for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do
   esac
 fi
 # Use eval to expand $SHELL
-if eval "$MISSING --is-lightweight"; then
-  am_missing_run="$MISSING "
+if eval "$MISSING --run true"; then
+  am_missing_run="$MISSING --run "
 else
   am_missing_run=
   { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: 'missing' script is too old or missing" >&5
 fi
 rmdir .tst 2>/dev/null
 
-@%:@ Check whether --enable-silent-rules was given.
-if test "${enable_silent_rules+set}" = set; then :
-  enableval=$enable_silent_rules; 
-fi
-
-case $enable_silent_rules in @%:@ (((
-  yes) AM_DEFAULT_VERBOSITY=0;;
-   no) AM_DEFAULT_VERBOSITY=1;;
-    *) AM_DEFAULT_VERBOSITY=1;;
-esac
-am_make=${MAKE-make}
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $am_make supports nested variables" >&5
-$as_echo_n "checking whether $am_make supports nested variables... " >&6; }
-if ${am_cv_make_support_nested_variables+:} false; then :
-  $as_echo_n "(cached) " >&6
-else
-  if $as_echo 'TRUE=$(BAR$(V))
-BAR0=false
-BAR1=true
-V=1
-am__doit:
-	@$(TRUE)
-.PHONY: am__doit' | $am_make -f - >/dev/null 2>&1; then
-  am_cv_make_support_nested_variables=yes
-else
-  am_cv_make_support_nested_variables=no
-fi
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_make_support_nested_variables" >&5
-$as_echo "$am_cv_make_support_nested_variables" >&6; }
-if test $am_cv_make_support_nested_variables = yes; then
-    AM_V='$(V)'
-  AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
-else
-  AM_V=$AM_DEFAULT_VERBOSITY
-  AM_DEFAULT_V=$AM_DEFAULT_VERBOSITY
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-AM_BACKSLASH='\'
-
 if test "`cd $srcdir && pwd`" != "`pwd`"; then
   # Use -I$(srcdir) only when $(srcdir) != ., so that make's output
   # is not polluted with repeated "-I."
   $as_echo_n "(cached) " >&6
 else
   
-	for am_cv_pathless_PYTHON in python python2 python3 python3.3 python3.2 python3.1 python3.0 python2.7  python2.6 python2.5 python2.4 python2.3 python2.2 python2.1 python2.0 none; do
+	for am_cv_pathless_PYTHON in python python2 python3 python3.2 python3.1 python3.0 python2.7  python2.6 python2.5 python2.4 python2.3 python2.2 python2.1 python2.0 none; do
 	  test "$am_cv_pathless_PYTHON" = none && break
 	  prog="import sys
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   PYTHON_PLATFORM=$am_cv_python_platform
 
 
-  # Just factor out some code duplication.
-  am_python_setup_sysconfig="\
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-# Prefer sysconfig over distutils.sysconfig, for better compatibility
-# with python 3.x.  See automake bug#10227.
-try:
-    import sysconfig
-except ImportError:
-    can_use_sysconfig = 0
-else:
-    can_use_sysconfig = 1
-# Can't use sysconfig in CPython 2.7, since it's broken in virtualenvs:
-# <https://github.com/pypa/virtualenv/issues/118>
-try:
-    from platform import python_implementation
-    if python_implementation() == 'CPython' and sys.version[:3] == '2.7':
-        can_use_sysconfig = 0
-except ImportError:
-    pass"
 
   
             { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $am_display_PYTHON script directory" >&5
      else
        am_py_prefix=$prefix
      fi
-     am_cv_python_pythondir=`$PYTHON -c "
-$am_python_setup_sysconfig
-if can_use_sysconfig:
-    sitedir = sysconfig.get_path('purelib', vars={'base':'$am_py_prefix'})
-else:
-    from distutils import sysconfig
-    sitedir = sysconfig.get_python_lib(0, 0, prefix='$am_py_prefix')
-sys.stdout.write(sitedir)"`
+     am_cv_python_pythondir=`$PYTHON -c "import sys; from distutils import sysconfig; sys.stdout.write(sysconfig.get_python_lib(0,0,prefix='$am_py_prefix'))" 2>/dev/null`
      case $am_cv_python_pythondir in
      $am_py_prefix*)
        am__strip_prefix=`echo "$am_py_prefix" | sed 's|.|.|g'`
      else
        am_py_exec_prefix=$exec_prefix
      fi
-     am_cv_python_pyexecdir=`$PYTHON -c "
-$am_python_setup_sysconfig
-if can_use_sysconfig:
-    sitedir = sysconfig.get_path('platlib', vars={'platbase':'$am_py_prefix'})
-else:
-    from distutils import sysconfig
-    sitedir = sysconfig.get_python_lib(1, 0, prefix='$am_py_prefix')
-sys.stdout.write(sitedir)"`
+     am_cv_python_pyexecdir=`$PYTHON -c "import sys; from distutils import sysconfig; sys.stdout.write(sysconfig.get_python_lib(1,0,prefix='$am_py_exec_prefix'))" 2>/dev/null`
      case $am_cv_python_pyexecdir in
      $am_py_exec_prefix*)
        am__strip_prefix=`echo "$am_py_exec_prefix" | sed 's|.|.|g'`

autom4te.cache/output.1

 build_vendor
 build_cpu
 build
-AM_BACKSLASH
-AM_DEFAULT_VERBOSITY
-AM_DEFAULT_V
-AM_V
 am__untar
 am__tar
 AMTAR
 ac_subst_files=''
 ac_user_opts='
 enable_option_checking
-enable_silent_rules
 '
       ac_precious_vars='build_alias
 host_alias
    esac
   cat <<\_ACEOF
 
-Optional Features:
-  --disable-option-checking  ignore unrecognized --enable/--with options
-  --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no)
-  --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]
-  --enable-silent-rules   less verbose build output (undo: "make V=1")
-  --disable-silent-rules  verbose build output (undo: "make V=0")
-
 Some influential environment variables:
   PYTHON      the Python interpreter
 
 
 
 
-am__api_version='1.13'
+am__api_version='1.12'
 
 ac_aux_dir=
 for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do
   esac
 fi
 # Use eval to expand $SHELL
-if eval "$MISSING --is-lightweight"; then
-  am_missing_run="$MISSING "
+if eval "$MISSING --run true"; then
+  am_missing_run="$MISSING --run "
 else
   am_missing_run=
   { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: 'missing' script is too old or missing" >&5
 fi
 rmdir .tst 2>/dev/null
 
-@%:@ Check whether --enable-silent-rules was given.
-if test "${enable_silent_rules+set}" = set; then :
-  enableval=$enable_silent_rules; 
-fi
-
-case $enable_silent_rules in @%:@ (((
-  yes) AM_DEFAULT_VERBOSITY=0;;
-   no) AM_DEFAULT_VERBOSITY=1;;
-    *) AM_DEFAULT_VERBOSITY=1;;
-esac
-am_make=${MAKE-make}
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $am_make supports nested variables" >&5
-$as_echo_n "checking whether $am_make supports nested variables... " >&6; }
-if ${am_cv_make_support_nested_variables+:} false; then :
-  $as_echo_n "(cached) " >&6
-else
-  if $as_echo 'TRUE=$(BAR$(V))
-BAR0=false
-BAR1=true
-V=1
-am__doit:
-	@$(TRUE)
-.PHONY: am__doit' | $am_make -f - >/dev/null 2>&1; then
-  am_cv_make_support_nested_variables=yes
-else
-  am_cv_make_support_nested_variables=no
-fi
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_make_support_nested_variables" >&5
-$as_echo "$am_cv_make_support_nested_variables" >&6; }
-if test $am_cv_make_support_nested_variables = yes; then
-    AM_V='$(V)'
-  AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
-else
-  AM_V=$AM_DEFAULT_VERBOSITY
-  AM_DEFAULT_V=$AM_DEFAULT_VERBOSITY
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-AM_BACKSLASH='\'
-
 if test "`cd $srcdir && pwd`" != "`pwd`"; then
   # Use -I$(srcdir) only when $(srcdir) != ., so that make's output
   # is not polluted with repeated "-I."
   $as_echo_n "(cached) " >&6
 else
   
-	for am_cv_pathless_PYTHON in python python2 python3 python3.3 python3.2 python3.1 python3.0 python2.7  python2.6 python2.5 python2.4 python2.3 python2.2 python2.1 python2.0 none; do
+	for am_cv_pathless_PYTHON in python python2 python3 python3.2 python3.1 python3.0 python2.7  python2.6 python2.5 python2.4 python2.3 python2.2 python2.1 python2.0 none; do
 	  test "$am_cv_pathless_PYTHON" = none && break
 	  prog="import sys
 # split strings by '.' and convert to numeric.  Append some zeros
   PYTHON_PLATFORM=$am_cv_python_platform
 
 
-  # Just factor out some code duplication.
-  am_python_setup_sysconfig="\
-import sys
-# Prefer sysconfig over distutils.sysconfig, for better compatibility
-# with python 3.x.  See automake bug#10227.
-try:
-    import sysconfig
-except ImportError:
-    can_use_sysconfig = 0
-else:
-    can_use_sysconfig = 1
-# Can't use sysconfig in CPython 2.7, since it's broken in virtualenvs:
-# <https://github.com/pypa/virtualenv/issues/118>
-try:
-    from platform import python_implementation
-    if python_implementation() == 'CPython' and sys.version[:3] == '2.7':
-        can_use_sysconfig = 0
-except ImportError:
-    pass"
 
   
             { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $am_display_PYTHON script directory" >&5
      else
        am_py_prefix=$prefix
      fi
-     am_cv_python_pythondir=`$PYTHON -c "
-$am_python_setup_sysconfig
-if can_use_sysconfig:
-    sitedir = sysconfig.get_path('purelib', vars={'base':'$am_py_prefix'})
-else:
-    from distutils import sysconfig
-    sitedir = sysconfig.get_python_lib(0, 0, prefix='$am_py_prefix')
-sys.stdout.write(sitedir)"`
+     am_cv_python_pythondir=`$PYTHON -c "import sys; from distutils import sysconfig; sys.stdout.write(sysconfig.get_python_lib(0,0,prefix='$am_py_prefix'))" 2>/dev/null`
      case $am_cv_python_pythondir in
      $am_py_prefix*)
        am__strip_prefix=`echo "$am_py_prefix" | sed 's|.|.|g'`
      else
        am_py_exec_prefix=$exec_prefix
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-     am_cv_python_pyexecdir=`$PYTHON -c "
-$am_python_setup_sysconfig
-if can_use_sysconfig:
-    sitedir = sysconfig.get_path('platlib', vars={'platbase':'$am_py_prefix'})
-else:
-    from distutils import sysconfig
-    sitedir = sysconfig.get_python_lib(1, 0, prefix='$am_py_prefix')
-sys.stdout.write(sitedir)"`
+     am_cv_python_pyexecdir=`$PYTHON -c "import sys; from distutils import sysconfig; sys.stdout.write(sysconfig.get_python_lib(1,0,prefix='$am_py_exec_prefix'))" 2>/dev/null`
      case $am_cv_python_pyexecdir in
      $am_py_exec_prefix*)
        am__strip_prefix=`echo "$am_py_exec_prefix" | sed 's|.|.|g'`

autom4te.cache/output.2

 build_vendor
 build_cpu
 build
-AM_BACKSLASH
-AM_DEFAULT_VERBOSITY
-AM_DEFAULT_V
-AM_V
 am__untar
 am__tar
 AMTAR
 ac_subst_files=''
 ac_user_opts='
 enable_option_checking
-enable_silent_rules
 '
       ac_precious_vars='build_alias
 host_alias
    esac
   cat <<\_ACEOF
 
-Optional Features:
-  --disable-option-checking  ignore unrecognized --enable/--with options
-  --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no)
-  --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]
-  --enable-silent-rules   less verbose build output (undo: "make V=1")
-  --disable-silent-rules  verbose build output (undo: "make V=0")
-
 Some influential environment variables:
   PYTHON      the Python interpreter
 
 
 
 
-am__api_version='1.13'
+am__api_version='1.12'
 
 ac_aux_dir=
 for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do
   esac
 fi
 # Use eval to expand $SHELL
-if eval "$MISSING --is-lightweight"; then
-  am_missing_run="$MISSING "
+if eval "$MISSING --run true"; then
+  am_missing_run="$MISSING --run "
 else
   am_missing_run=
   { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: 'missing' script is too old or missing" >&5
 fi
 rmdir .tst 2>/dev/null
 
-@%:@ Check whether --enable-silent-rules was given.
-if test "${enable_silent_rules+set}" = set; then :
-  enableval=$enable_silent_rules; 
-fi
-
-case $enable_silent_rules in @%:@ (((
-  yes) AM_DEFAULT_VERBOSITY=0;;
-   no) AM_DEFAULT_VERBOSITY=1;;
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-am_make=${MAKE-make}
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $am_make supports nested variables" >&5
-$as_echo_n "checking whether $am_make supports nested variables... " >&6; }
-if ${am_cv_make_support_nested_variables+:} false; then :
-  $as_echo_n "(cached) " >&6
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-  if $as_echo 'TRUE=$(BAR$(V))
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-	for am_cv_pathless_PYTHON in python python2 python3 python3.3 python3.2 python3.1 python3.0 python2.7  python2.6 python2.5 python2.4 python2.3 python2.2 python2.1 python2.0 none; do
+	for am_cv_pathless_PYTHON in python python2 python3 python3.2 python3.1 python3.0 python2.7  python2.6 python2.5 python2.4 python2.3 python2.2 python2.1 python2.0 none; do
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-else:
-    from distutils import sysconfig
-    sitedir = sysconfig.get_python_lib(0, 0, prefix='$am_py_prefix')
-sys.stdout.write(sitedir)"`
+     am_cv_python_pythondir=`$PYTHON -c "import sys; from distutils import sysconfig; sys.stdout.write(sysconfig.get_python_lib(0,0,prefix='$am_py_prefix'))" 2>/dev/null`
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-else:
-    from distutils import sysconfig
-    sitedir = sysconfig.get_python_lib(1, 0, prefix='$am_py_prefix')
-sys.stdout.write(sitedir)"`
+     am_cv_python_pyexecdir=`$PYTHON -c "import sys; from distutils import sysconfig; sys.stdout.write(sysconfig.get_python_lib(1,0,prefix='$am_py_exec_prefix'))" 2>/dev/null`
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autom4te.cache/requests

                       '0',
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                       [
-                        '/usr/local/Cellar/autoconf/2.69/share/autoconf'
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                       ],
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-                        '/usr/local/Cellar/autoconf/2.69/share/autoconf/autoconf/autoconf.m4f',
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-                        '/usr/local/Cellar/automake/1.13.1/share/aclocal-1.13/tar.m4',
+                        '/gpfs/runtime/opt/centos-updates/6.3/share/autoconf/autoconf/autoconf.m4f',
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+                        '/gpfs/runtime/opt/centos-updates/6.3/share/aclocal-1.12/cond.m4',
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+                        '/gpfs/runtime/opt/centos-updates/6.3/share/aclocal-1.12/depout.m4',
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+                        '/gpfs/runtime/opt/centos-updates/6.3/share/aclocal-1.12/options.m4',
+                        '/gpfs/runtime/opt/centos-updates/6.3/share/aclocal-1.12/python.m4',
+                        '/gpfs/runtime/opt/centos-updates/6.3/share/aclocal-1.12/runlog.m4',
+                        '/gpfs/runtime/opt/centos-updates/6.3/share/aclocal-1.12/sanity.m4',
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+                        '/gpfs/runtime/opt/centos-updates/6.3/share/aclocal-1.12/substnot.m4',
+                        '/gpfs/runtime/opt/centos-updates/6.3/share/aclocal-1.12/tar.m4',
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                         'configure.ac'
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                         '_AM_DEPENDENCIES' => 1,
-                        'm4_include' => 1,
                         'AM_PROG_INSTALL_SH' => 1,
-                        'AM_PATH_PYTHON' => 1,
+                        'm4_include' => 1,
                         '_AC_AM_CONFIG_HEADER_HOOK' => 1,
+                        'AM_PATH_PYTHON' => 1,
                         'AU_DEFUN' => 1,
                         'AM_MAKE_INCLUDE' => 1
                       }
                       '1',
                       1,
                       [
-                        '/usr/local/Cellar/autoconf/2.69/share/autoconf',
+                        '/gpfs/runtime/opt/centos-updates/6.3/share/autoconf',
                         'm4'
                       ],
                       [
-                        '/usr/local/Cellar/autoconf/2.69/share/autoconf/autoconf/autoconf.m4f',
+                        '/gpfs/runtime/opt/centos-updates/6.3/share/autoconf/autoconf/autoconf.m4f',
                         'aclocal.m4',
                         'configure.ac'
                       ],
                       '2',
                       1,
                       [
-                        '/usr/local/Cellar/autoconf/2.69/share/autoconf'
+                        '/gpfs/runtime/opt/centos-updates/6.3/share/autoconf'
                       ],
                       [
-                        '/usr/local/Cellar/autoconf/2.69/share/autoconf/autoconf/autoconf.m4f',
+                        '/gpfs/runtime/opt/centos-updates/6.3/share/autoconf/autoconf/autoconf.m4f',
                         'aclocal.m4',
                         'configure.ac'
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-m4trace:/usr/local/Cellar/automake/1.13.1/share/aclocal-1.13/python.m4:219: -1- AC_DEFUN([AM_PATH_PYTHON], [
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   m4_define_default([_AM_PYTHON_INTERPRETER_LIST],
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   dnl Set up 4 directories:
 
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        am_py_prefix=$prefix
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-    from distutils import sysconfig
-    sitedir = sysconfig.get_python_lib(0, 0, prefix='$am_py_prefix')
-sys.stdout.write(sitedir)"`
+     am_cv_python_pythondir=`$PYTHON -c "import sys; from distutils import sysconfig; sys.stdout.write(sysconfig.get_python_lib(0,0,prefix='$am_py_prefix'))" 2>/dev/null`
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-else:
-    from distutils import sysconfig
-    sitedir = sysconfig.get_python_lib(1, 0, prefix='$am_py_prefix')
-sys.stdout.write(sitedir)"`
+     am_cv_python_pyexecdir=`$PYTHON -c "import sys; from distutils import sysconfig; sys.stdout.write(sysconfig.get_python_lib(1,0,prefix='$am_py_exec_prefix'))" 2>/dev/null`
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-m4trace:/usr/local/Cellar/automake/1.13.1/share/aclocal-1.13/python.m4:239: -1- AC_DEFUN([AM_PYTHON_CHECK_VERSION], [prog="import sys
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autom4te.cache/traces.1

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-#   2011, 2012, 2013 Free Software Foundation, Inc.
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 # under the terms of the GNU General Public License as published by
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+# the same distribution terms that you use for the rest of that program.
+
+
+# Originally written by Per Bothner.  Please send patches (context
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+# exits with 0.  Otherwise, it exits with 1.
 #
 # You can get the latest version of this script from:
 # http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
-#
-# Please send patches with a ChangeLog entry to config-patches@gnu.org.
-
 
 me=`echo "$0" | sed -e 's,.*/,,'`
 
 
 Originally written by Per Bothner.
 Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000,
-2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011,
-2012, 2013 Free Software Foundation, Inc.
+2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012
+Free Software Foundation, Inc.
 
 This is free software; see the source for copying conditions.  There is NO
 warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
     arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*)
 	echo arm-acorn-riscix${UNAME_RELEASE}
 	exit ;;
-    arm*:riscos:*:*|arm*:RISCOS:*:*)
+    arm:riscos:*:*|arm:RISCOS:*:*)
 	echo arm-unknown-riscos
 	exit ;;
     SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*)
 # Configuration validation subroutine script.
 #   Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
 #   2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010,
-#   2011, 2012, 2013 Free Software Foundation, Inc.
+#   2011, 2012 Free Software Foundation, Inc.
 
-timestamp='2012-12-29'
+timestamp='2012-08-18'
 
-# This file is free software; you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 3 of the License, or
+# This file is (in principle) common to ALL GNU software.
+# The presence of a machine in this file suggests that SOME GNU software
+# can handle that machine.  It does not imply ALL GNU software can.
+#
+# This file is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
 # (at your option) any later version.
 #
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-# General Public License for more details.
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
 #
 # You should have received a copy of the GNU General Public License
 # along with this program; if not, see <http://www.gnu.org/licenses/>.
 # As a special exception to the GNU General Public License, if you
 # distribute this file as part of a program that contains a
 # configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that
-# program.  This Exception is an additional permission under section 7
-# of the GNU General Public License, version 3 ("GPLv3").
+# the same distribution terms that you use for the rest of that program.
 
 
-# Please send patches with a ChangeLog entry to config-patches@gnu.org.
+# Please send patches to <config-patches@gnu.org>.  Submit a context
+# diff and a properly formatted GNU ChangeLog entry.
 #
 # Configuration subroutine to validate and canonicalize a configuration type.
 # Supply the specified configuration type as an argument.
 GNU config.sub ($timestamp)
 
 Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000,
-2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011,
-2012, 2013 Free Software Foundation, Inc.
+2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012
+Free Software Foundation, Inc.
 
 This is free software; see the source for copying conditions.  There is NO
 warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
 	-convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\
 	-c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \
 	-harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \
-	-apple | -axis | -knuth | -cray | -microblaze*)
+	-apple | -axis | -knuth | -cray | -microblaze)
 		os=
 		basic_machine=$1
 		;;
 	| alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \
 	| alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \
 	| am33_2.0 \
-	| arc \
-	| arm | arm[bl]e | arme[lb] | armv[2-8] | armv[3-8][lb] | armv7[arm] \
-	| avr | avr32 \
-	| be32 | be64 \
+	| arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr | avr32 \
+        | be32 | be64 \
 	| bfin \
 	| c4x | clipper \
 	| d10v | d30v | dlx | dsp16xx \
 	| le32 | le64 \
 	| lm32 \
 	| m32c | m32r | m32rle | m68000 | m68k | m88k \
-	| maxq | mb | microblaze | microblazeel | mcore | mep | metag \
+	| maxq | mb | microblaze | mcore | mep | metag \
 	| mips | mipsbe | mipseb | mipsel | mipsle \
 	| mips16 \
 	| mips64 | mips64el \
 	| lm32-* \
 	| m32c-* | m32r-* | m32rle-* \
 	| m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \
-	| m88110-* | m88k-* | maxq-* | mcore-* | metag-* \
-	| microblaze-* | microblazeel-* \
+	| m88110-* | m88k-* | maxq-* | mcore-* | metag-* | microblaze-* \
 	| mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \
 	| mips16-* \
 	| mips64-* | mips64el-* \
 		basic_machine=ns32k-utek
 		os=-sysv
 		;;
-	microblaze*)
+	microblaze)
 		basic_machine=microblaze-xilinx
 		;;
 	mingw64)
 		basic_machine=i586-unknown
 		os=-pw32
 		;;
-	rdos | rdos64)
-		basic_machine=x86_64-pc
-		os=-rdos
-		;;
-	rdos32)
+	rdos)
 		basic_machine=i386-pc
 		os=-rdos
 		;;
 build_vendor
 build_cpu
 build
-AM_BACKSLASH
-AM_DEFAULT_VERBOSITY
-AM_DEFAULT_V
-AM_V
 am__untar
 am__tar
 AMTAR
 ac_subst_files=''
 ac_user_opts='
 enable_option_checking
-enable_silent_rules
 '
       ac_precious_vars='build_alias
 host_alias
    esac
   cat <<\_ACEOF
 
-Optional Features:
-  --disable-option-checking  ignore unrecognized --enable/--with options
-  --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no)
-  --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]
-  --enable-silent-rules   less verbose build output (undo: "make V=1")
-  --disable-silent-rules  verbose build output (undo: "make V=0")
-
 Some influential environment variables:
   PYTHON      the Python interpreter