--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastx_toolkit-0.0.6/configure.ac	Thu Aug 14 04:52:17 2014 -0400
@@ -0,0 +1,92 @@
+# Copyright (C) 2008 Assaf Gordon <gordon@cshl.edu>
+#  
+# This file is free software; as a special exception the author 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.
+
+AC_INIT([FASTX Toolkit],
+        [0.0.6],
+        [Assaf Gordon gordon@cshl.edu],
+        [fastx_toolkit])
+AC_CONFIG_AUX_DIR(config)
+AM_CONFIG_HEADER(config.h)
+AM_INIT_AUTOMAKE([dist-bzip2])
+
+# 23dec08, Gordon
+# Only added those things because 'autoheader' was complaining...
+AC_DEFINE([CXX_HAS_BUGGY_FOR_LOOPS], [], [Description])
+AC_DEFINE([CXX_HAS_NO_BOOL], [], [Description])
+AC_DEFINE([NDEBUG], [], [Description])
+AC_DEFINE([YOUR_OS], [], [Description])
+
+dnl --enable-wall
+EXTRA_CHECKS="-Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror"
+AC_ARG_ENABLE(wall,
+[  --enable-wall          Enable many common GCC warnings (-Wall,-Wextra, -Werror etc., default enabled)],
+[case "${enableval}" in
+  yes) wall=true ;;
+  no)  wall=false ;;
+  *) AC_MSG_ERROR(bad value ${enableval} for --enable-wall) ;;
+esac],[wall=true])
+if test "$wall" = "true"
+then
+  CFLAGS="${CFLAGS} ${EXTRA_CHECKS}"
+  CXXFLAGS="${CXXFLAGS} ${EXTRA_CHECKS}"
+fi
+
+dnl --enable-debug
+AC_ARG_ENABLE(debug,
+[  --enable-debug          Enable debug mode (default enabled)],
+[case "${enableval}" in
+  yes) debug=true ;;
+  no)  debug=false ;;
+  *) AC_MSG_ERROR(bad value ${enableval} for --enable-debug) ;;
+esac],[debug=true])
+if test "$debug" = "true"
+then
+  CFLAGS="${CFLAGS} -DDEBUG -g -O1"
+  CXXFLAGS="${CFLAGS} -DDEBUG -g -O1"
+else
+  CFLAGS="${CFLAGS} -O3"
+  CXXFLAGS="${CFLAGS} -O3"
+fi
+
+
+LF_CONFIGURE_CC
+LF_CONFIGURE_CXX
+LF_HOST_TYPE
+LF_SET_WARNINGS
+AC_PROG_RANLIB
+
+AC_CONFIG_FILES([
+   Makefile
+   doc/Makefile
+   m4/Makefile
+   src/Makefile
+   src/libfastx/Makefile
+   src/fastx_clipper/Makefile
+   src/fastq_to_fasta/Makefile
+   src/fastx_quality_stats/Makefile
+   src/fastq_quality_converter/Makefile
+   src/fastx_trimmer/Makefile
+   src/fastq_quality_filter/Makefile
+   src/fastx_artifacts_filter/Makefile
+   src/fastx_reverse_complement/Makefile
+   src/fastx_collapser/Makefile
+   src/seqalign_test/Makefile
+   galaxy/Makefile
+   galaxy/tools/Makefile
+   galaxy/tools/fastx_toolkit/Makefile
+   galaxy/tools/fastx_toolkit_with_gzip_and_output_label/Makefile
+   galaxy/test-data/Makefile
+   galaxy/static/Makefile
+   galaxy/static/fastx_icons/Makefile
+   galaxy/tool-data/Makefile
+   scripts/Makefile
+])
+
+AC_OUTPUT