diff -up EMBOSS-6.6.0/ajax/acd/Makefile.am.system-pcre EMBOSS-6.6.0/ajax/acd/Makefile.am
--- EMBOSS-6.6.0/ajax/acd/Makefile.am.system-pcre	2013-07-15 17:25:27.000000000 -0400
+++ EMBOSS-6.6.0/ajax/acd/Makefile.am	2015-10-30 09:48:28.603257770 -0400
@@ -7,10 +7,10 @@ libacd_la_CFLAGS = $(WARN_CFLAGS) $(DEVW
 libacd_la_CPPFLAGS  = -I$(top_srcdir)/ajax/ajaxdb
 libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
 libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
-libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 if !ESYSTEMLIBS
 libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
 libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
+libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 endif
 libacd_la_CPPFLAGS += -I$(top_srcdir)/plplot
 libacd_la_CPPFLAGS += $(JAVA_CPPFLAGS)
diff -up EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am.system-pcre EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am
--- EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am.system-pcre	2013-07-15 17:25:28.000000000 -0400
+++ EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am	2015-10-30 09:48:28.603257770 -0400
@@ -5,10 +5,10 @@ lib_LTLIBRARIES = libajaxdb.la
 libajaxdb_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
 
 libajaxdb_la_CPPFLAGS  = -I$(top_srcdir)/ajax/ensembl
-libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 if !ESYSTEMLIBS
 libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
 libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
+libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 endif
 libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/plplot
 libajaxdb_la_CPPFLAGS += $(AXIS2C_CPPFLAGS)
diff -up EMBOSS-6.6.0/ajax/core/ajreg.h.system-pcre EMBOSS-6.6.0/ajax/core/ajreg.h
--- EMBOSS-6.6.0/ajax/core/ajreg.h.system-pcre	2011-10-18 10:23:40.000000000 -0400
+++ EMBOSS-6.6.0/ajax/core/ajreg.h	2015-10-30 09:48:28.603257770 -0400
@@ -39,9 +39,8 @@
 #include "ajdefine.h"
 #include "ajstr.h"
 
-#include "pcre_config.h"
-#include "pcre_internal.h"
-#include "pcreposix.h"
+#include <pcre.h>
+#include <pcreposix.h>
 
 AJ_BEGIN_DECLS
 
@@ -84,7 +83,7 @@ AJ_BEGIN_DECLS
 
 typedef struct AjSRegexp
 {
-    real_pcre *pcre;
+    struct real_pcre *pcre;
     pcre_extra *extra;
     int *ovector;
     const char* orig;
diff -up EMBOSS-6.6.0/ajax/core/Makefile.am.system-pcre EMBOSS-6.6.0/ajax/core/Makefile.am
--- EMBOSS-6.6.0/ajax/core/Makefile.am.system-pcre	2013-07-15 17:25:28.000000000 -0400
+++ EMBOSS-6.6.0/ajax/core/Makefile.am	2015-10-30 09:49:05.159002139 -0400
@@ -4,10 +4,11 @@ lib_LTLIBRARIES = libajax.la
 
 libajax_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
 
-libajax_la_CPPFLAGS  = -I$(top_srcdir)/ajax/pcre
+libajax_la_CPPFLAGS  =
 if !ESYSTEMLIBS
 libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
 libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
+libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 endif
 libajax_la_CPPFLAGS += -I$(top_srcdir)/plplot
 libajax_la_CPPFLAGS += $(JAVA_CPPFLAGS)
diff -up EMBOSS-6.6.0/ajax/ensembl/Makefile.am.system-pcre EMBOSS-6.6.0/ajax/ensembl/Makefile.am
--- EMBOSS-6.6.0/ajax/ensembl/Makefile.am.system-pcre	2013-07-15 17:25:31.000000000 -0400
+++ EMBOSS-6.6.0/ajax/ensembl/Makefile.am	2015-10-30 09:49:24.304868253 -0400
@@ -4,10 +4,11 @@ lib_LTLIBRARIES = libensembl.la
 
 libensembl_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
 
-libensembl_la_CPPFLAGS  = -I$(top_srcdir)/ajax/pcre
+libensembl_la_CPPFLAGS  =
 if !ESYSTEMLIBS
 libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
 libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
+libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 endif
 libensembl_la_CPPFLAGS += -I$(top_srcdir)/plplot
 libensembl_la_CPPFLAGS += $(JAVA_CPPFLAGS)
diff -up EMBOSS-6.6.0/ajax/graphics/Makefile.am.system-pcre EMBOSS-6.6.0/ajax/graphics/Makefile.am
--- EMBOSS-6.6.0/ajax/graphics/Makefile.am.system-pcre	2013-07-15 17:25:33.000000000 -0400
+++ EMBOSS-6.6.0/ajax/graphics/Makefile.am	2015-10-30 09:49:52.210673110 -0400
@@ -4,9 +4,10 @@ lib_LTLIBRARIES = libajaxg.la
 
 libajaxg_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
 
-libajaxg_la_CPPFLAGS  = -I$(top_srcdir)/ajax/pcre
+libajaxg_la_CPPFLAGS  =
 if !ESYSTEMLIBS
 libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
+libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 endif
 libajaxg_la_CPPFLAGS += -I$(top_srcdir)/plplot
 libajaxg_la_CPPFLAGS += $(JAVA_CPPFLAGS)
diff -up EMBOSS-6.6.0/ajax/Makefile.am.system-pcre EMBOSS-6.6.0/ajax/Makefile.am
--- EMBOSS-6.6.0/ajax/Makefile.am.system-pcre	2011-08-25 15:45:55.000000000 -0400
+++ EMBOSS-6.6.0/ajax/Makefile.am	2015-10-30 09:48:28.604257763 -0400
@@ -1,7 +1,7 @@
 ## Process this file with automake to produce Makefile.in
 
-SUBDIRS  = pcre
+SUBDIRS  =
 if !ESYSTEMLIBS
-SUBDIRS += expat zlib
+SUBDIRS += expat zlib pcre
 endif
 SUBDIRS += core graphics ensembl ajaxdb acd
diff -up EMBOSS-6.6.0/configure.in.system-pcre EMBOSS-6.6.0/configure.in
--- EMBOSS-6.6.0/configure.in.system-pcre	2013-07-15 17:25:27.000000000 -0400
+++ EMBOSS-6.6.0/configure.in	2015-10-30 09:48:28.604257763 -0400
@@ -630,31 +630,6 @@ AS_CASE([${host_os}],
 
 
 
-dnl PCRE library definitions - see the MAJOR and MINOR values
-dnl to see which version's configure.in these lines come from
-
-dnl Provide the current PCRE version information. Do not use numbers
-dnl with leading zeros for the minor version, as they end up in a C
-dnl macro, and may be treated as octal constants. Stick to single
-dnl digits for minor numbers less than 10. There are unlikely to be
-dnl that many releases anyway.
-
-PCRE_MAJOR="7"
-PCRE_MINOR="9"
-PCRE_DATE="11-Apr-2009"
-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
-
-dnl Default values for miscellaneous macros
-
-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
-
-dnl Provide versioning information for libtool shared libraries that
-dnl are built by default on Unix systems.
-
-PCRE_LIB_VERSION="0:1:0"
-PCRE_POSIXLIB_VERSION="0:0:0"
-
-
 dnl Define where the EMBOSS package is located
 AC_SUBST([AJAX_FIXED_ROOT])
 AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\""
@@ -743,19 +718,6 @@ AX_LIB_POSTGRESQL
 
 
 
-dnl "Export" these variables for PCRE
-
-AC_SUBST([HAVE_MEMMOVE])
-AC_SUBST([HAVE_STRERROR])
-AC_SUBST([PCRE_MAJOR])
-AC_SUBST([PCRE_MINOR])
-AC_SUBST([PCRE_DATE])
-AC_SUBST([PCRE_VERSION])
-AC_SUBST([PCRE_LIB_VERSION])
-AC_SUBST([PCRE_POSIXLIB_VERSION])
-AC_SUBST([POSIX_MALLOC_THRESHOLD])
-
-
 
 
 # Enable debugging: --enable-debug, sets CFLAGS
@@ -846,7 +808,9 @@ AS_IF([test "x${enable_large}" = "xno"],
 
 AC_ARG_ENABLE([systemlibs],
 [AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles])])
-
+if test "x${enable_systemlibs}" = "xyes" ; then
+   AC_CHECK_LIB(pcre, pcre_compile)
+fi
 AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
 
 
@@ -1000,7 +964,6 @@ AC_CONFIG_FILES([Makefile
                  ajax/ensembl/Makefile
                  ajax/expat/Makefile
                  ajax/graphics/Makefile
-                 ajax/pcre/Makefile
                  ajax/zlib/Makefile
                  doc/Makefile
                  doc/manuals/Makefile
diff -up EMBOSS-6.6.0/emboss/Makefile.am.system-pcre EMBOSS-6.6.0/emboss/Makefile.am
--- EMBOSS-6.6.0/emboss/Makefile.am.system-pcre	2013-07-15 17:25:46.000000000 -0400
+++ EMBOSS-6.6.0/emboss/Makefile.am	2015-10-30 09:48:28.605257756 -0400
@@ -30,10 +30,10 @@ AM_CPPFLAGS  = -I$(top_srcdir)/ajax/acd
 AM_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb
 AM_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
 AM_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
-AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 if !ESYSTEMLIBS
 AM_CPPFLAGS += -I$(top_srcdir)/ajax/expat
 AM_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
+AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 endif
 AM_CPPFLAGS += -I$(top_srcdir)/nucleus
 AM_CPPFLAGS += -I$(top_srcdir)/plplot
@@ -49,8 +49,8 @@ LDADD += ../ajax/core/libajax.la
 if !ESYSTEMLIBS
 LDADD += ../ajax/zlib/libezlib.la
 LDADD += ../ajax/expat/libeexpat.la
-endif
 LDADD += ../ajax/pcre/libepcre.la
+endif
 LDADD += ../plplot/libeplplot.la
 LDADD += $(XLIB)
 
diff -up EMBOSS-6.6.0/nucleus/Makefile.am.system-pcre EMBOSS-6.6.0/nucleus/Makefile.am
--- EMBOSS-6.6.0/nucleus/Makefile.am.system-pcre	2013-07-15 17:25:50.000000000 -0400
+++ EMBOSS-6.6.0/nucleus/Makefile.am	2015-10-30 09:48:28.605257756 -0400
@@ -11,10 +11,10 @@ endif
 endif
 
 libnucleus_la_CPPFLAGS  = -I$(top_srcdir)/plplot
-libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 if !ESYSTEMLIBS
 libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
 libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
+libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 endif
 libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
 libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl