Version Bump #335603, Unbundled libs, removed old, fix clash with /usr/bin/digest, #330507

(Portage version: 2.2.0_alpha26/cvs/Linux x86_64)

8 files changed, 837 insertions, 59 deletions

diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index 7e96b832e72f..3b0859c74147 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -1,6 +1,15 @@
 # ChangeLog for sci-biology/emboss
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.58 2010/07/18 14:17:56 nixnut Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.59 2011/03/09 12:00:38 jlec Exp $
+
+*emboss-6.3.1 (09 Mar 2011)
+
+  09 Mar 2011; Justin Lecher <jlec@gentoo.org>
+  +files/6.3.1-unbundle-libs.patch, +files/emboss-README.Gentoo-2,
+  emboss-4.0.0.ebuild, emboss-6.0.1.ebuild, emboss-6.1.0-r1.ebuild,
+  +emboss-6.3.1.ebuild, metadata.xml:
+  Version Bump #335603, Unbundled libs, removed old, fix clash with
+  /usr/bin/digest, #330507
 
   18 Jul 2010; <nixnut@gentoo.org> emboss-6.0.1.ebuild:
   ppc stable #325457
diff --git a/sci-biology/emboss/emboss-4.0.0.ebuild b/sci-biology/emboss/emboss-4.0.0.ebuild
index 45108c0c8d75..73fd33c954f8 100644
--- a/sci-biology/emboss/emboss-4.0.0.ebuild
+++ b/sci-biology/emboss/emboss-4.0.0.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-4.0.0.ebuild,v 1.13 2010/06/23 12:03:44 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-4.0.0.ebuild,v 1.14 2011/03/09 12:00:38 jlec Exp $
 
 EAPI=1
 
@@ -13,12 +13,13 @@ SLOT="0"
 KEYWORDS="amd64 ppc ppc64 ~sparc x86"
 IUSE="X png minimal"
 
-DEPEND="X? ( x11-libs/libXt )
+DEPEND="
+	X? ( x11-libs/libXt )
 	png? (
 		sys-libs/zlib
 		media-libs/libpng
-		>=media-libs/gd-1.8
-	)
+		media-libs/gd
+		)
 	!minimal? (
 		sci-biology/primer3
 		sci-biology/clustalw:1
@@ -28,23 +29,25 @@ DEPEND="X? ( x11-libs/libXt )
 RDEPEND="${DEPEND}
 	!sys-devel/cons"
 
-PDEPEND="!minimal? (
+PDEPEND="
+	!minimal? (
 		sci-biology/aaindex
 		sci-biology/cutg
 		sci-biology/prints
-		>=sci-biology/prosite-19.7
-		>=sci-biology/rebase-601-r1
+		sci-biology/prosite
+		sci-biology/rebase
 		sci-biology/transfac
 	)"
 
 S="${WORKDIR}/EMBOSS-${PV}"
 
 src_compile() {
-	EXTRA_CONF="--includedir=${D}/usr/include/emboss"
-	! use X && EXTRA_CONF="${EXTRA_CONF} --without-x"
-	! use png && EXTRA_CONF="${EXTRA_CONF} --without-pngdriver"
+	local myconf
+	myconf="--includedir=${D}/usr/include/emboss"
+	use X || myconf="${EXTRA_CONF} --without-x"
+	use png || myconf="${EXTRA_CONF} --without-pngdriver"
 
-	econf ${EXTRA_CONF} || die
+	econf ${myconf}
 	# Do not install the JEMBOSS component (the --without-java configure option
 	# does not work). JEMBOSS will eventually be available as a separate package.
 	sed -i -e 's/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/' \
@@ -67,21 +70,21 @@ src_install() {
 	dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials || die
 	dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html || die
 
+	# Clashes #330507
+	mv "${ED}"/usr/bin/{digest,pepdigest} || die
+
 	# Remove useless dummy files from the image.
-	rm "${D}"/usr/share/EMBOSS/data/{AAINDEX,PRINTS,PROSITE,REBASE}/dummyfile \
-			|| die "Failed to remove dummy files."
+	find emboss/data -name dummyfile -delete || die "Failed to remove dummy files."
 
 	# Move the provided codon files to a different directory. This will avoid
 	# user confusion and file collisions on case-insensitive file systems (see
 	# bug #115446). This change is documented in "README.Gentoo".
-	mv "${D}"/usr/share/EMBOSS/data/CODONS \
-			"${D}"/usr/share/EMBOSS/data/CODONS.orig || \
+	mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
 			die "Failed to move CODON directory."
 
 	# Move the provided restriction enzyme prototypes file to a different name.
 	# This will avoid file collisions with future versions of rebase that will
 	# install their own enzyme prototypes file (see bug #118832).
-	mv "${D}"/usr/share/EMBOSS/data/embossre.equ \
-			"${D}"/usr/share/EMBOSS/data/embossre.equ.orig || \
+	mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \
 			die "Failed to move enzyme equivalence file."
 }
diff --git a/sci-biology/emboss/emboss-6.0.1.ebuild b/sci-biology/emboss/emboss-6.0.1.ebuild
index 75f955ba1d0c..5173f966ff1b 100644
--- a/sci-biology/emboss/emboss-6.0.1.ebuild
+++ b/sci-biology/emboss/emboss-6.0.1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.0.1.ebuild,v 1.6 2010/07/18 14:17:56 nixnut Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.0.1.ebuild,v 1.7 2011/03/09 12:00:38 jlec Exp $
 
 EAPI=1
 
@@ -15,26 +15,28 @@ SLOT="0"
 KEYWORDS="amd64 ppc ppc64 ~sparc x86"
 IUSE="X png minimal"
 
-DEPEND="X? ( x11-libs/libXt )
+DEPEND="
+	X? ( x11-libs/libXt )
 	png? (
 		sys-libs/zlib
 		media-libs/libpng
 		media-libs/gd
-	)
+		)
 	!minimal? (
 		sci-biology/primer3
-		sci-biology/clustalw:1
-	)"
+		sci-biology/clustalw
+		)"
 
 RDEPEND="${DEPEND}
 	!sys-devel/cons"
 
-PDEPEND="!minimal? (
+PDEPEND="
+	!minimal? (
 		sci-biology/aaindex
 		sci-biology/cutg
 		sci-biology/prints
 		sci-biology/prosite
-		>=sci-biology/rebase-707
+		sci-biology/rebase
 		sci-biology/transfac
 	)"
 
@@ -45,20 +47,21 @@ src_unpack() {
 	cd "${S}"
 	epatch "${FILESDIR}"/${PN}-5.0.0-as-needed.patch
 
-	local link_string="-lX11";
+	local link_string="$(pkg-config --libs x11)"
 	if use png; then
-		link_string="${link_string} -lgd -lpng"
+		link_string="${link_string} -lgd $(pkg-config --libs libpng)"
 	fi
 	sed -e "s:PATCH_PLPLOT:${link_string}:" -i plplot/Makefile.in \
 		|| die "Failed to patch ajax Makefile"
 }
 
 src_compile() {
-	EXTRA_CONF="--includedir=${D}/usr/include/emboss"
-	! use X && EXTRA_CONF="${EXTRA_CONF} --without-x"
-	! use png && EXTRA_CONF="${EXTRA_CONF} --without-pngdriver"
+	local myconf
+	myconf="--includedir=${D}/usr/include/emboss"
+	use X || myconf="${EXTRA_CONF} --without-x"
+	use png || myconf="${EXTRA_CONF} --without-pngdriver"
 
-	econf ${EXTRA_CONF} || die
+	econf ${myconf}
 	# Do not install the JEMBOSS component (the --without-java configure option
 	# does not work). JEMBOSS will eventually be available as a separate package.
 	sed -i -e "s/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/" \
@@ -89,21 +92,21 @@ src_install() {
 	dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials || die
 	dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html || die
 
+	# Clashes #330507
+	mv "${ED}"/usr/bin/{digest,pepdigest} || die
+
 	# Remove useless dummy files from the image.
-	rm "${D}"/usr/share/EMBOSS/data/{AAINDEX,PRINTS,PROSITE,REBASE}/dummyfile \
-			|| die "Failed to remove dummy files."
+	find emboss/data -name dummyfile -delete || die "Failed to remove dummy files."
 
 	# Move the provided codon files to a different directory. This will avoid
 	# user confusion and file collisions on case-insensitive file systems (see
 	# bug #115446). This change is documented in "README.Gentoo".
-	mv "${D}"/usr/share/EMBOSS/data/CODONS \
-			"${D}"/usr/share/EMBOSS/data/CODONS.orig || \
+	mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
 			die "Failed to move CODON directory."
 
 	# Move the provided restriction enzyme prototypes file to a different name.
 	# This avoids file collisions with versions of rebase that install their
 	# own enzyme prototypes file (see bug #118832).
-	mv "${D}"/usr/share/EMBOSS/data/embossre.equ \
-			"${D}"/usr/share/EMBOSS/data/embossre.equ.orig || \
+	mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \
 			die "Failed to move enzyme equivalence file."
 }
diff --git a/sci-biology/emboss/emboss-6.1.0-r1.ebuild b/sci-biology/emboss/emboss-6.1.0-r1.ebuild
index 8a32a9352ae1..4af8ef3e3142 100644
--- a/sci-biology/emboss/emboss-6.1.0-r1.ebuild
+++ b/sci-biology/emboss/emboss-6.1.0-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.1.0-r1.ebuild,v 1.2 2010/06/23 12:03:44 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.1.0-r1.ebuild,v 1.3 2011/03/09 12:00:38 jlec Exp $
 
 EAPI="3"
 
@@ -15,26 +15,28 @@ SLOT="0"
 KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
 IUSE="X png minimal"
 
-DEPEND="X? ( x11-libs/libXt )
+DEPEND="
+	X? ( x11-libs/libXt )
 	png? (
 		sys-libs/zlib
 		media-libs/libpng
 		media-libs/gd
-	)
+		)
 	!minimal? (
 		sci-biology/primer3
 		sci-biology/clustalw
-	)"
+		)"
 
 RDEPEND="${DEPEND}
 	!sys-devel/cons"
 
-PDEPEND="!minimal? (
+PDEPEND="
+	!minimal? (
 		sci-biology/aaindex
 		sci-biology/cutg
 		sci-biology/prints
 		sci-biology/prosite
-		>=sci-biology/rebase-707
+		sci-biology/rebase
 		sci-biology/transfac
 	)"
 
@@ -43,20 +45,21 @@ S="${WORKDIR}/EMBOSS-${PV}"
 src_prepare() {
 	epatch "${FILESDIR}"/${PN}-5.0.0-as-needed.patch
 
-	local link_string="-lX11";
+	local link_string="$(pkg-config --libs x11)"
 	if use png; then
-		link_string="${link_string} -lgd -lpng"
+		link_string="${link_string} -lgd $(pkg-config --libs libpng)"
 	fi
 	sed -e "s:PATCH_PLPLOT:${link_string}:" -i plplot/Makefile.in \
 		|| die "Failed to patch ajax Makefile"
 }
 
 src_configure() {
-	EXTRA_CONF="--includedir=${ED}/usr/include/emboss"
-	! use X && EXTRA_CONF="${EXTRA_CONF} --without-x"
-	! use png && EXTRA_CONF="${EXTRA_CONF} --without-pngdriver"
+	local myconf
+	myconf="--includedir=${ED}/usr/include/emboss"
+	use X || myconf="${EXTRA_CONF} --without-x"
+	use png || myconf="${EXTRA_CONF} --without-pngdriver"
 
-	econf ${EXTRA_CONF} || die
+	econf ${myconf}
 	# Do not install the JEMBOSS component (the --without-java configure option
 	# does not work). JEMBOSS will eventually be available as a separate package.
 	sed -i -e "s/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/" \
@@ -91,21 +94,21 @@ src_install() {
 	rm "${ED}"/usr/share/EMBOSS/doc/programs/text/frestdist.txt || \
 			die "Failed to remove duplicated documentation."
 
+	# Clashes #330507
+	mv "${ED}"/usr/bin/{digest,pepdigest} || die
+
 	# Remove useless dummy files from the image.
-	rm "${ED}"/usr/share/EMBOSS/data/{AAINDEX,PRINTS,PROSITE,REBASE}/dummyfile \
-			|| die "Failed to remove dummy files."
+	find emboss/data -name dummyfile -delete || die "Failed to remove dummy files."
 
 	# Move the provided codon files to a different directory. This will avoid
 	# user confusion and file collisions on case-insensitive file systems (see
 	# bug #115446). This change is documented in "README.Gentoo".
-	mv "${ED}"/usr/share/EMBOSS/data/CODONS \
-			"${ED}"/usr/share/EMBOSS/data/CODONS.orig || \
+	mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
 			die "Failed to move CODON directory."
 
 	# Move the provided restriction enzyme prototypes file to a different name.
 	# This avoids file collisions with versions of rebase that install their
 	# own enzyme prototypes file (see bug #118832).
-	mv "${ED}"/usr/share/EMBOSS/data/embossre.equ \
-			"${ED}"/usr/share/EMBOSS/data/embossre.equ.orig || \
+	mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \
 			die "Failed to move enzyme equivalence file."
 }
diff --git a/sci-biology/emboss/emboss-6.3.1.ebuild b/sci-biology/emboss/emboss-6.3.1.ebuild
new file mode 100644
index 000000000000..e7f52c4dbb4e
--- /dev/null
+++ b/sci-biology/emboss/emboss-6.3.1.ebuild
@@ -0,0 +1,123 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.3.1.ebuild,v 1.1 2011/03/09 12:00:38 jlec Exp $
+
+EAPI="4"
+
+inherit autotools eutils
+
+DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
+HOMEPAGE="http://emboss.sourceforge.net/"
+SRC_URI="ftp://${PN}.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz"
+LICENSE="GPL-2 LGPL-2"
+
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+IUSE="doc +largefile minimal mysql pdf png postgres static-libs X"
+
+DEPEND="
+	dev-libs/expat
+	dev-libs/libpcre:3
+	sci-libs/plplot
+	sys-libs/zlib
+	mysql? ( dev-db/mysql )
+	pdf? ( media-libs/libharu )
+	png? (
+		sys-libs/zlib
+		media-libs/libpng
+		media-libs/gd
+		)
+	postgres? ( dev-db/postgresql-base )
+	!minimal? (
+		sci-biology/primer3
+		sci-biology/clustalw
+		)
+	X? ( x11-libs/libXt )"
+RDEPEND="${DEPEND}
+	!sys-devel/cons"
+PDEPEND="
+	!minimal? (
+		sci-biology/aaindex
+		sci-biology/cutg
+		sci-biology/prints
+		sci-biology/prosite
+		sci-biology/rebase
+		sci-biology/transfac
+		)"
+
+S="${WORKDIR}/EMBOSS-${PV}"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PV}-unbundle-libs.patch
+	eautoreconf
+}
+
+conf-with() {
+	# USE with-option Option
+	if use ${1}; then
+		echo "--with-${2}=${3}"
+	else
+		echo "--without-${2}"
+	fi
+}
+
+src_configure() {
+	local myconf
+	myconf="--includedir=${ED}/usr/include/emboss --enable-systemlibs"
+
+	myconf="${myconf} $(conf-with png pngdriver ${EPREFIX}/usr)"
+	myconf="${myconf} $(conf-with doc docroot ${EPREFIX}/usr)"
+	myconf="${myconf} $(conf-with pdf hpdf ${EPREFIX}/usr)"
+	myconf="${myconf} $(conf-with mysql mysql ${EPREFIX}/usr/bin/mysql_config)"
+	myconf="${myconf} $(conf-with postgresql postgresql ${EPREFIX}/usr/bin/pg_config)"
+
+	econf \
+		$(use_with X x) \
+		$(use_enable amd64 64) \
+		$(use_enable largefile large) \
+		$(use_enable static-libs static) \
+		--without-java \
+		${myconf}
+}
+
+src_install() {
+	einstall || die "Failed to install program files."
+
+	dodoc AUTHORS ChangeLog FAQ NEWS README THANKS
+	sed "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \
+	dodoc README.Gentoo
+
+	# Install env file for setting libplplot and acd files path.
+	cat <<- EOF > 22emboss
+		# plplot libs dir
+		PLPLOT_LIB="${EPREFIX}/usr/share/EMBOSS/"
+		# ACD files location
+		EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd"
+	EOF
+	doenvd 22emboss
+
+	# Symlink preinstalled docs to "/usr/share/doc".
+	dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals
+	dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs
+	dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials
+	dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html
+
+	# Clashes #330507
+	mv "${ED}"/usr/bin/{digest,pepdigest} || die
+
+	# Remove useless dummy files from the image.
+	find emboss/data -name dummyfile -delete || die "Failed to remove dummy files."
+
+	# Move the provided codon files to a different directory. This will avoid
+	# user confusion and file collisions on case-insensitive file systems (see
+	# bug #115446). This change is documented in "README.Gentoo".
+	mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
+			die "Failed to move CODON directory."
+
+	# Move the provided restriction enzyme prototypes file to a different name.
+	# This avoids file collisions with versions of rebase that install their
+	# own enzyme prototypes file (see bug #118832).
+	mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \
+			die "Failed to move enzyme equivalence file."
+}
diff --git a/sci-biology/emboss/files/6.3.1-unbundle-libs.patch b/sci-biology/emboss/files/6.3.1-unbundle-libs.patch
new file mode 100644
index 000000000000..5e463744a739
--- /dev/null
+++ b/sci-biology/emboss/files/6.3.1-unbundle-libs.patch
@@ -0,0 +1,600 @@
+diff --git a/Makefile.am b/Makefile.am
+index 4fe2ed1..7f3a95f 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -5,12 +5,21 @@ ACLOCAL_AMFLAGS = -I m4
+ 
+ AUTOMAKE_OPTIONS = gnits
+ 
+-SUBDIRS = plplot ajax nucleus emboss test doc jemboss
++if !ESYSTEMLIBS
++EXTRA_DIRS = plplot
++endif
++
++if GJEMBOSS
++JEMBOSS_DIR = jemboss
++endif
++
++SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR)
++DIST_SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR)
+ 
+ # AJAX_FIXED_ROOT = \"`pwd`/emboss/acd\"
+ 
+ # files with nonstandard names in this directory
+-EXTRA_DIST = COMPAT LICENSE KNOWN_BUGS ONEWS PROBLEMS FAQ ChangeLog depcomp ltmain.sh
++EXTRA_DIST = COMPAT KNOWN_BUGS ONEWS PROBLEMS FAQ ChangeLog depcomp ltmain.sh
+ 
+ # tar to pick up the other directories
+ # then remove any CVS subdirectories
+diff --git a/README.fixes b/README.fixes
+new file mode 100644
+index 0000000..3c56d79
+--- /dev/null
++++ b/README.fixes
+@@ -0,0 +1,9 @@
++The files in this directory are bugfix replacements for files in
++the EMBOSS-6.3.1 distribution. Just drop the replacement files in
++the location shown and redo the 'make install.'
++
++Fix 1. EMBOSS-6.3.1/configure
++       EMBOSS-6.3.1/m4/mysql.m4
++
++21 Jul 2010: Addresses a problem whereby, in some circumstances, inclusion of
++             hpdf support prevented inclusion of MySQL support.
+diff --git a/ajax/Makefile.am b/ajax/Makefile.am
+index 4a44f6f..cf27ff8 100644
+--- a/ajax/Makefile.am
++++ b/ajax/Makefile.am
+@@ -1,6 +1,6 @@
+ ## Process this file with automake to produce Makefile.in
+ if !ESYSTEMLIBS
+-EXTRA_DIRS = expat zlib
++EXTRA_DIRS = pcre expat zlib
+ endif
+ 
+-SUBDIRS = pcre $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
++SUBDIRS = $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
+diff --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am
+index 02bcaa7..368ddfe 100644
+--- a/ajax/acd/Makefile.am
++++ b/ajax/acd/Makefile.am
+@@ -13,10 +13,13 @@ CYGWIN_LDACD = -L../../plplot -L../pcre -L../expat -L../zlib -L../core \
+ endif
+ 
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
++else
++EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
+ endif
+ 
+-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
++INCLUDES =  \
+ $(EXTRA_INCLUDES) \
+ -I$(top_srcdir)/ajax/core \
+ -I$(top_srcdir)/ajax/graphics \
+@@ -38,3 +41,4 @@ LINKFLAGS = $(VERS_INF)
+ endif
+ 
+ libacd_la_LDFLAGS = $(LINKFLAGS)
++libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la ../ajaxdb/libajaxdb.la
+diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am
+index da57727..857ca5f 100644
+--- a/ajax/ajaxdb/Makefile.am
++++ b/ajax/ajaxdb/Makefile.am
+@@ -13,11 +13,12 @@ CYGWIN_LDAJAXDB = -L../../plplot -L../pcre -L../expat -L../zlib -L../core \
+ endif
+ 
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
+ endif
+ 
+ 
+-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
++INCLUDES = \
+ $(EXTRA_INCLUDES) \
+ -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/ensembl
+ 
+@@ -37,3 +38,4 @@ LINKFLAGS = $(VERS_INF)
+ endif
+ 
+ libajaxdb_la_LDFLAGS = $(LINKFLAGS)
++libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la
+diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am
+index af27cb0..8fa4a3a 100644
+--- a/ajax/core/Makefile.am
++++ b/ajax/core/Makefile.am
+@@ -12,13 +12,18 @@ CYGWIN_LDAJAX = -L../../plplot -L../expat -L../pcre -L../zlib \
+ endif
+ 
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre 
++else
++EXTRA_LIBS = -lexpat -lpcre
+ endif
+ 
++EXTRA_DIST = ajax-pcre-config.h.in
++DISTCLEAN = ajax-pcre-config.h
+ 
+ INCLUDES = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) \
+ -DAJAX_SYSTEM="$(AJAX_SYSTEM)" -DPREFIX=\"$(prefix)\" \
+--I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre $(EXTRA_INCLUDES)
++$(EXTRA_INCLUDES) $(POSTGRESQL_CFLAGS) $(MYSQL_CFLAGS)
+ 
+ AJAXSRC = ajalign.c ajarr.c ajassert.c \
+ ajbase.c ajcall.c ajcod.c \
+@@ -44,7 +49,7 @@ ajindex.h ajjava.h ajlist.h \
+ ajmath.h ajmatrices.h ajmem.h ajmess.h \
+ ajnam.h ajnexus.h ajobo.h \
+ ajpat.h ajpdb.h ajpdbio.h ajphylo.h \
+-ajrange.h ajreg.h ajreport.h ajresource.h \
++ajrange.h ajreg.h ajax-pcre-config.h ajreport.h ajresource.h \
+ ajseq.h ajseqabi.h ajseqbam.h ajseqdata.h ajseqread.h ajseqtype.h ajseqwrite.h \
+ ajsort.h ajsql.h ajstr.h ajsys.h \
+ ajtable.h ajtax.h ajtime.h ajtranslate.h ajtree.h ajutil.h ajvector.h
+@@ -61,3 +66,4 @@ LINKFLAGS = $(VERS_INF)
+ endif
+ 
+ libajax_la_LDFLAGS = $(LINKFLAGS)
++libajax_la_LIBADD = $(EXTRA_LIBS) $(POSTGRESQL_LDFLAGS) $(MYSQL_LDFLAGS)
+diff --git a/ajax/core/ajax-pcre-config.h.in b/ajax/core/ajax-pcre-config.h.in
+new file mode 100644
+index 0000000..b09e4e6
+--- /dev/null
++++ b/ajax/core/ajax-pcre-config.h.in
+@@ -0,0 +1 @@
++@DEFINE_USE_SYSTEM_PCRE@ AJAX_USE_SYSTEM_PCRE
+diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h
+index 06793be..659f462 100644
+--- a/ajax/core/ajreg.h
++++ b/ajax/core/ajreg.h
+@@ -16,9 +16,14 @@ extern "C"
+ #define ajreg_h
+ 
+ #include "ajax.h"
++#include "ajax-pcre-config.h"
++#ifndef AJAX_USE_SYSTEM_PCRE
+ #include "pcre_config.h"
+ #include "pcre_internal.h"
+ #include "pcreposix.h"
++#else
++#include <pcre.h>
++#endif
+ 
+ #define AJREG_OVECSIZE 30
+ 
+@@ -41,7 +46,11 @@ extern "C"
+ ******************************************************************************/
+ 
+ typedef struct AjSRegexp {
++#ifndef AJAX_USE_SYSTEM_PCRE
+     real_pcre *pcre;
++#else
++    pcre *pcre;
++#endif
+     pcre_extra *extra;
+     int *ovector;
+     const char* orig;
+diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am
+index ca33a84..87e51bd 100644
+--- a/ajax/ensembl/Makefile.am
++++ b/ajax/ensembl/Makefile.am
+@@ -10,12 +10,13 @@ CYGWIN_LDENSEMBL = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplo
+ endif
+ 
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre 
+ endif
+ 
+ 
+-INCLUDES = -I$(top_srcdir)/plplot $(EXTRA_INCLUDES) \
+--I$(top_srcdir)/ajax/pcre -I$(top_srcdir)/ajax/core
++INCLUDES = $(EXTRA_INCLUDES) \
++-I$(top_srcdir)/ajax/core
+ 
+ ENSEMBLSRC = ensanalysis.c ensassembly.c ensassemblyexception.c \
+ ensassemblymapper.c ensattribute.c ensbaseadaptor.c enscache.c \
+@@ -56,3 +57,4 @@ LINKFLAGS = $(VERS_INF)
+ endif
+ 
+ libensembl_la_LDFLAGS = $(LINKFLAGS)
++libensembl_la_LIBADD = ../core/libajax.la
+diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am
+index ab45afc..f61c605 100644
+--- a/ajax/graphics/Makefile.am
++++ b/ajax/graphics/Makefile.am
+@@ -10,11 +10,15 @@ CYGWIN_LDAJAXG = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplot
+ endif
+ 
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
++else
++EXTRA_INCLUDES = $(PLPLOT_CFLAGS) -DUSE_PLXSFNAM_SHIM
++EXTRA_LIBS = $(PLPLOT_LIBS)
+ endif
+ 
+ 
+-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
++INCLUDES = \
+ $(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core
+ 
+ AJAXGSRC = ajgraph.c ajhist.c
+@@ -32,3 +36,4 @@ LINKFLAGS = $(VERS_INF)
+ endif
+ 
+ libajaxg_la_LDFLAGS = $(LINKFLAGS)
++libajaxg_la_LIBADD = ../core/libajax.la $(EXTRA_LIBS)
+diff --git a/ajax/graphics/ajgraph.c b/ajax/graphics/ajgraph.c
+index 25e75e4..60f2743 100644
+--- a/ajax/graphics/ajgraph.c
++++ b/ajax/graphics/ajgraph.c
+@@ -34,10 +34,8 @@
+ #include <float.h>
+ #define AZ 28
+ 
+-
+ #include "plplotP.h"
+ 
+-
+ static void     GraphArray(ajuint numofpoints,
+ 			   float *x, float *y);
+ static void     GraphArrayGaps(ajuint numofpoints,
+@@ -1049,13 +1047,26 @@ static void GraphDefCharSize(float size)
+ ** @@
+ ******************************************************************************/
+ 
++#define _GNU_SOURCE
++#include <stdio.h>
++
+ static void GraphSetName(const AjPGraph thys,
+ 			 const AjPStr txt, const char *ext)
+ {
+     if(!thys->ready)
+     {
++#ifdef USE_PLXSFNAM_SHIM
++        char *fullname;
++#endif
+         ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext);
++#ifdef USE_PLXSFNAM_SHIM
++        fullname = asprintf(fullname,"%s%s", ajStrGetPtr(txt), ext);
++        ajDebug("=g= plsfnam ('%S') instead\n", fullname);
++        plsfnam(fullname);
++        free(fullname);
++#else
+         plxsfnam(ajStrGetPtr(txt), ext);
++#endif
+         ajStrAssignS(&graphBasename, txt);
+         ajStrAssignC(&graphExtension, ext);
+         if(ajStrGetCharFirst(graphExtension) == '.')
+diff --git a/configure.in b/configure.in
+index ddb4f81..3f4fe5e 100644
+--- a/configure.in
++++ b/configure.in
+@@ -235,15 +235,6 @@ AC_PROG_INSTALL
+ AC_PROG_LN_S
+ AC_PROG_MAKE_SET
+ 
+-dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+-if test "${with_x}" != "no" ; then
+-if test "`uname -a | grep Darwin`"; then
+-OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'`
+-if test ${OSXX} '>' '10.4'; then
+-CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib"
+-fi
+-fi
+-fi
+ 
+ # Checks for header files.
+ #as# AC_PATH_X
+@@ -292,9 +283,6 @@ AC_CHECK_FUNCS(memmove)
+ #as# 		select socket sqrt strchr strcspn strdup strerror strpbrk \
+ #as# 		strrchr strspn strstr strtol])
+ 
+-if test "${with_x}" != "no" ; then
+-LF_EMBOSS_PATH_XLIB
+-fi
+ 
+ dnl Library checks
+ AC_CHECK_LIB(c, socket, LIBS="$LIBS" , LIBS="$LIBS -lsocket")
+@@ -316,14 +304,16 @@ CHECK_PNGDRIVER
+ CHECK_AUTH
+ CHECK_AMD64
+ 
++AM_CONDITIONAL(GJEMBOSS, test "$JAVA_OK" = "yes")
++
+ AX_LIB_MYSQL
+ AX_LIB_POSTGRESQL
+ 
+ CFLAGS="$CFLAGS $MYSQL_CFLAGS"
+ LDFLAGS="$LDFLAGS $MYSQL_LDFLAGS"
+ 
+-CFLAGS="$CFLAGS $POSTGRESQL_CFLAGS"
+-LDFLAGS="$LDFLAGS $POSTGRESQL_LDFLAGS"
++CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS"
++LDFLAGS="$POSTGRESQL_LDFLAGS $LDFLAGS"
+ 
+ 
+ dnl Check for 'ant' for packaging Jemboss and export result
+@@ -443,13 +433,36 @@ fi
+ 
+ dnl Test if --enable-systemlibs given
+ have_systemlibs=no
++DEFINE_USE_SYSTEM_PCRE="#undef"
+ AC_ARG_ENABLE(systemlibs,
+    AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles]))
++AC_MSG_CHECKING(for systemlib usage)
+ if test "${enable_systemlibs}" = "yes" ; then
+     have_systemlibs=yes
++    DEFINE_USE_SYSTEM_PCRE="#define"
++    PKG_CHECK_MODULES([PLPLOT], [plplotd])
++    PKG_CHECK_MODULES([ZLIB], [zlib])
++else
++    dnl X11 is only used by plplot
++    dnl Intel MacOSX 10.6 puts X11 in a non-standard place
++    if test "${with_x}" != "no" ; then
++    if test "`uname -a | grep Darwin`"; then
++    OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'`
++    if test ${OSXX} '>' '10.4'; then
++    CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib"
++    fi
++    fi
++    fi
++    if test "${with_x}" != "no" ; then
++    LF_EMBOSS_PATH_XLIB
++    fi
++     AC_MSG_NOTICE(USING bundled LIBS)
+ fi          
+ AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes")
+ AC_SUBST(ESYSTEMLIBS)
++AC_SUBST(DEFINE_USE_SYSTEM_PCRE)
++AC_SUBST(PLPLOT_CFLAGS)
++AC_SUBST(PLPLOT_LIBS)
+ 
+ 
+ 
+@@ -457,7 +470,6 @@ AC_SUBST(ESYSTEMLIBS)
+ 
+ dnl Test if purify exists and if --enable-purify given if so
+ dnl set "-g"
+-
+ AC_MSG_CHECKING(for purify)
+ dnl if(purify -version) < /dev/null > /dev/null 2>&1; then
+    AC_ARG_ENABLE(purify,
+@@ -683,6 +695,7 @@ CHECK_THREADS
+ 
+ 
+ AC_OUTPUT([plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile
++ajax/core/ajax-pcre-config.h
+ ajax/pcre/Makefile ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile
+ ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile
+ ajax/acd/Makefile
+diff --git a/emboss/Makefile.am b/emboss/Makefile.am
+index 0820517..a0257b2 100644
+--- a/emboss/Makefile.am
++++ b/emboss/Makefile.am
+@@ -79,14 +79,17 @@ wordcount wordfinder wordmatch wossname \
+ yank
+ 
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
++else
++EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
+ endif
+ 
+-INCLUDES = -I$(top_srcdir)/nucleus -I$(top_srcdir)/ajax/pcre \
++INCLUDES = -I$(top_srcdir)/nucleus \
+ 	$(EXTRA_INCLUDES) \
+ 	-I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \
+ 	-I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
+-	-I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot
++	-I$(top_srcdir)/ajax/acd
+ 
+ 
+ aaindexextract_SOURCES = aaindexextract.c
+@@ -319,7 +322,7 @@ testplot_SOURCES = testplot.c
+ treetypedisplay_SOURCES = treetypedisplay.c
+ 
+ if !ESYSTEMLIBS
+-EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la
++EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la ../plplot/libeplplot.la ../ajax/pcre/libepcre.la
+ endif
+ 
+ 
+@@ -327,7 +330,6 @@ LDADD = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \
+ 	../ajax/ajaxdb/libajaxdb.la ../ajax/ensembl/libensembl.la \
+ 	../ajax/graphics/libajaxg.la ../ajax/core/libajax.la \
+ 	$(EXTRA_LDS) \
+-	../ajax/pcre/libepcre.la ../plplot/libeplplot.la \
+ 	$(XLIB)
+ 
+ pkgdata_DATA = emboss.default.template
+diff --git a/m4/mysql.m4 b/m4/mysql.m4
+index fe413af..ebea25c 100644
+--- a/m4/mysql.m4
++++ b/m4/mysql.m4
+@@ -1,4 +1,6 @@
+-##### http://autoconf-archive.cryp.to/ax_lib_mysql.html
++# ===========================================================================
++#       http://www.gnu.org/software/autoconf-archive/ax_lib_mysql.html
++# ===========================================================================
+ #
+ # SYNOPSIS
+ #
+@@ -6,19 +8,18 @@
+ #
+ # DESCRIPTION
+ #
+-#   This macro provides tests of availability of MySQL client library
+-#   of particular version or newer.
++#   This macro provides tests of availability of MySQL client library of
++#   particular version or newer.
+ #
+-#   AX_LIB_MYSQL macro takes only one argument which is optional. If
+-#   there is no required version passed, then macro does not run
+-#   version test.
++#   AX_LIB_MYSQL macro takes only one argument which is optional. If there
++#   is no required version passed, then macro does not run version test.
+ #
+ #   The --with-mysql option takes one of three possible values:
+ #
+ #   no - do not check for MySQL client library
+ #
+-#   yes - do check for MySQL library in standard locations
+-#   (mysql_config should be in the PATH)
++#   yes - do check for MySQL library in standard locations (mysql_config
++#   should be in the PATH)
+ #
+ #   path - complete path to mysql_config utility, use this option if
+ #   mysql_config can't be found in the PATH
+@@ -33,27 +34,23 @@
+ #
+ #     HAVE_MYSQL
+ #
+-# LAST MODIFICATION
++# LICENSE
+ #
+-#   2006-07-16
+-#   2007-01-09 MS: mysql_config --cflags may set gcc -fomit-frame-pointers,
+-#                  which prevents gdb from displaying stack traces.
+-#                  Changed mysql_config --cflags to mysql_config --include
++#   Copyright (c) 2008 Mateusz Loskot <mateusz@loskot.net>
+ #
+-# COPYLEFT
+-#
+-#   Copyright (c) 2006 Mateusz Loskot <mateusz@loskot.net>
+-#
+-#   Copying and distribution of this file, with or without
+-#   modification, are permitted in any medium without royalty provided
+-#   the copyright notice and this notice are preserved.
++#   Copying and distribution of this file, with or without modification, are
++#   permitted in any medium without royalty provided the copyright notice
++#   and this notice are preserved. This file is offered as-is, without any
++#   warranty.
++
++#serial 12
+ 
+ AC_DEFUN([AX_LIB_MYSQL],
+ [
+     AC_ARG_WITH([mysql],
+-        [AS_HELP_STRING([--with-mysql=@<:@ARG@:>@],
++        AS_HELP_STRING([--with-mysql=@<:@ARG@:>@],
+             [use MySQL client library @<:@default=yes@:>@, optionally specify path to mysql_config]
+-        )],
++        ),
+         [
+         if test "$withval" = "no"; then
+             want_mysql="no"
+@@ -66,19 +63,20 @@ AC_DEFUN([AX_LIB_MYSQL],
+         ],
+         [want_mysql="yes"]
+     )
++    AC_ARG_VAR([MYSQL_CONFIG], [Full path to mysql_config program])
+ 
+     MYSQL_CFLAGS=""
+     MYSQL_LDFLAGS=""
+     MYSQL_VERSION=""
+ 
+     dnl
+-    dnl Check MySQL libraries (libpq)
++    dnl Check MySQL libraries
+     dnl
+ 
+     if test "$want_mysql" = "yes"; then
+ 
+-        if test -z "$MYSQL_CONFIG" -o test; then
+-            AC_PATH_PROG([MYSQL_CONFIG], [mysql_config], [no])
++        if test -z "$MYSQL_CONFIG" ; then
++            AC_PATH_PROGS([MYSQL_CONFIG], [mysql_config mysql_config5], [no])
+         fi
+ 
+         if test "$MYSQL_CONFIG" != "no"; then
+@@ -90,35 +88,8 @@ dnl         MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`"
+ 
+             MYSQL_VERSION=`$MYSQL_CONFIG --version`
+ 
+-dnl It isn't enough to just test for mysql_config as Fedora
+-dnl provides it in the mysql RPM even though mysql-devel may
+-dnl not be installed
+-
+-    	    EMBCFLAGS=$CFLAGS
+-	    EMBLDFLAGS=$LDFLAGS
+-	    CFLAGS=$MYSQL_CFLAGS
+-	    LDFLAGS=$MYSQL_LDFLAGS
+-
+-            AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <stdio.h>
+-                                              #include "mysql.h"]],
+-					    [[mysql_info(NULL)]])],
+-			   [havemysql=yes],
+-			   [havemysql=no])
+-
+-	    CFLAGS=$EMBCFLAGS
+-	    LDFLAGS=$EMBLDFLAGS
+-
+-            if test "$havemysql" = yes; then
+-                AC_DEFINE([HAVE_MYSQL], [1],
+-                    [Define to 1 if MySQL libraries are available])
+-                found_mysql="yes"
+-                AC_MSG_RESULT([yes])
+-            else
+-	        MYSQL_CFLAGS=""
+-	        MYSQL_LDFLAGS=""
+-                found_mysql="no"
+-                AC_MSG_RESULT([no])
+-            fi
++            found_mysql="yes"
++            AC_MSG_RESULT([yes])
+         else
+             found_mysql="no"
+             AC_MSG_RESULT([no])
+@@ -170,6 +141,11 @@ dnl not be installed
+         fi
+     fi
+ 
++    if test "$found_mysql" = "yes" ; then
++        AC_DEFINE([HAVE_MYSQL], [1],
++                  [Define to 1 if MySQL libraries are available])
++    fi
++
+     AC_SUBST([MYSQL_VERSION])
+     AC_SUBST([MYSQL_CFLAGS])
+     AC_SUBST([MYSQL_LDFLAGS])
+diff --git a/nucleus/Makefile.am b/nucleus/Makefile.am
+index c244786..ff301b9 100644
+--- a/nucleus/Makefile.am
++++ b/nucleus/Makefile.am
+@@ -19,13 +19,16 @@ CYGWIN_LIBS = -L../plplot -L../ajax/pcre -L../ajax/expat -L../ajax/zlib \
+ -lezlib -leplplot
+ else
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
++else
++EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
+ endif
+ endif
+ 
+ 
+-INCLUDES = -I$(top_srcdir)/plplot $(X_CFLAGS) -I$(srcdir)/ \
+-	-I$(top_srcdir)/ajax -I$(top_srcdir)/ajax/pcre \
++INCLUDES = $(X_CFLAGS) -I$(srcdir)/ \
++	-I$(top_srcdir)/ajax \
+ 	$(EXTRA_INCLUDES) \
+ 	-I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \
+ 	-I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
+@@ -55,3 +58,4 @@ LINKFLAGS =  $(VERS_INF)
+ endif
+ 
+ libnucleus_la_LDFLAGS =  $(LINKFLAGS)
++libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/graphics/libajaxg.la ../ajax/acd/libacd.la
diff --git a/sci-biology/emboss/files/emboss-README.Gentoo-2 b/sci-biology/emboss/files/emboss-README.Gentoo-2
new file mode 100644
index 000000000000..72fa3662c9a8
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-README.Gentoo-2
@@ -0,0 +1,34 @@
+Administrating EMBOSS on Gentoo systems
+=======================================
+
+
+Codon data files location
+-------------------------
+
+The codon data files that are distributed with EMBOSS are installed in the
+``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual
+``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between
+these codon files and those installed with the CUTG database. The names of
+these files sometimes vary only by their case. Having both sets of files in
+the same directory is also impossible on systems such as MacOSX, where the
+root filesystem is case insensitive. If you do not have the CUTG database
+installed and want to use the codon files distributed with EMBOSS, you can
+symlink the ``CODONS.orig`` directory to ``CODONS``::
+
+	# cd EPREFIX/usr/share/EMBOSS/data
+	# ln -s CODONS.orig CODONS
+
+
+Restriction enzymes equivalence file location
+---------------------------------------------
+
+The restriction enzymes equivalence file distributed with EMBOSS is installed
+as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual
+``EPREFIX/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file
+collision with the equivalence file provided by the Rebase database. If you do
+not have the Rebase database installed and want to use the equivalence file
+distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to
+``embossre.equ``::
+
+	# cd EPREFIX/usr/share/EMBOSS/data
+	# ln -s embossre.equ.orig embossre.equ
diff --git a/sci-biology/emboss/metadata.xml b/sci-biology/emboss/metadata.xml
index b85761d07029..747e4ab37d3e 100644
--- a/sci-biology/emboss/metadata.xml
+++ b/sci-biology/emboss/metadata.xml
@@ -15,4 +15,7 @@
 		analysis into a seamless whole. EMBOSS breaks the historical trend
 		towards commercial software packages.
 	</longdescription>
+<use>
+  <flag name='largefile'>Support for large files</flag>
+</use>
 </pkgmetadata>