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From: "Justin Lecher" <jlec@gentoo.org>
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Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/files/, sci-biology/emboss/
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X-VCS-Files: sci-biology/emboss/ChangeLog sci-biology/emboss/emboss-6.3.1_p4.ebuild sci-biology/emboss/files/6.3.1_p4.patch sci-biology/emboss/files/emboss-README.Gentoo-2 sci-biology/emboss/metadata.xml
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commit:     895a849ade4a8dc6d5e0d49d6c8d8b5556eeca05
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Mar  9 18:37:54 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Mar  9 18:37:54 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc=
ommit;h=3D895a849a

Emboss-6.3.1 imported from tree

---
 sci-biology/emboss/ChangeLog                    |  299 +++++++++++
 sci-biology/emboss/emboss-6.3.1_p4.ebuild       |  116 +++++
 sci-biology/emboss/files/6.3.1_p4.patch         |  600 +++++++++++++++++=
++++++
 sci-biology/emboss/files/emboss-README.Gentoo-2 |   34 ++
 sci-biology/emboss/metadata.xml                 |   21 +
 5 files changed, 1070 insertions(+), 0 deletions(-)

diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
new file mode 100644
index 0000000..5d6f872
--- /dev/null
+++ b/sci-biology/emboss/ChangeLog
@@ -0,0 +1,299 @@
+# ChangeLog for sci-biology/emboss
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.61 2=
011/03/09 16:29:05 jlec Exp $
+
+  09 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4.ebuild:
+  EAPI=3D4 takes three arguments on use_with
+
+*emboss-6.3.1_p4 (09 Mar 2011)
+
+  09 Mar 2011; Justin Lecher <jlec@gentoo.org>
+  +files/6.3.1_p4-unbundle-libs.patch, -files/6.3.1-unbundle-libs.patch,
+  -emboss-6.3.1.ebuild, +emboss-6.3.1_p4.ebuild:
+  Bump to latest upstream patches
+
+*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
+
+  09 Jul 2010; Samuli Suominen <ssuominen@gentoo.org> emboss-6.0.1.ebuil=
d:
+  ppc64 stable wrt #325457
+
+  23 Jun 2010; Justin Lecher <jlec@gentoo.org> emboss-4.0.0.ebuild,
+  emboss-6.0.1.ebuild, emboss-6.1.0.ebuild, emboss-6.1.0-r1.ebuild:
+  Blocking sys-devel/cons, bug 248792
+
+*emboss-6.1.0-r1 (07 Mar 2010)
+
+  07 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+  +emboss-6.1.0-r1.ebuild:
+  Moved to EAPI=3D3 for PREFIX support, imported prefix patches from ove=
rlay,
+  keyworded as in overlay
+
+  01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
+  Giving up maintainership of this package.
+
+  01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> emboss-6.1.0.ebuild=
:
+  Remove documentation that conflicts with EMBASSY phylipnew.
+
+*emboss-6.1.0 (01 Sep 2009)
+
+  01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> +emboss-6.1.0.ebuil=
d:
+  New upstream version.
+
+  01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> emboss-6.0.1.ebuild=
:
+  Stabilised on x86 and amd64.
+
+  31 Aug 2009; Olivier Fisette <ribosome@gentoo.org> emboss-4.0.0.ebuild=
,
+  emboss-6.0.1.ebuild:
+  Q.A. fixes, including better dependency on ClustalW.
+
+  27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> -emboss-5.0.0.ebuil=
d:
+  Pruning version that will never be stabilised.
+
+  27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> emboss-4.0.0.ebuild=
:
+  Depend on ClustalW 1.83 since version 2.x will soon be added to Portag=
e
+  and is incompatible with EMBOSS wrapper programs.
+
+*emboss-6.0.1 (26 Aug 2008)
+
+  26 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +emboss-6.0.1.ebuil=
d:
+  New upstream version.
+
+  25 Jan 2008; Markus Dittrich <markusle@gentoo.org>
+  +files/emboss-5.0.0-as-needed.patch, emboss-4.0.0.ebuild,
+  emboss-5.0.0.ebuild:
+  Fixed unresolved symbols with as-needed (see bug #207304).
+
+  22 Jul 2007; Donnie Berkholz <dberkholz@gentoo.org>; emboss-4.0.0.ebui=
ld:
+  Drop virtual/x11 references.
+
+  18 Jul 2007; Olivier Fisette <ribosome@gentoo.org>
+  +files/emboss-README.Gentoo-1:
+  Added updated Gentoo README file in reStructuredText format.
+
+*emboss-5.0.0 (18 Jul 2007)
+
+  18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> +emboss-5.0.0.ebuil=
d:
+  New upstream version.
+
+  09 Apr 2007; Jeff Gardner <je_fro@gentoo.org> +files/22emboss,
+  -files/22emboss-r1, emboss-4.0.0.ebuild:
+  Fixed to use doenvd wrt bug #173884
+
+  10 Dec 2006; Olivier Fisette <ribosome@gentoo.org>
+  -emboss-3.0.0-r1.ebuild, emboss-4.0.0.ebuild:
+  Pruned old version. Removed ppc-macos keyword, as grobian said the
+  package and its dependencies were fully moved into "prefix".
+
+  20 Nov 2006; <blubb@gentoo.org> emboss-4.0.0.ebuild:
+  stable on amd64
+
+  15 Nov 2006; Markus Rothe <corsair@gentoo.org> emboss-4.0.0.ebuild:
+  Stable on ppc64; bug #153766
+
+  03 Nov 2006; nixnut <nixnut@gentoo.org> emboss-4.0.0.ebuild:
+  Stable on ppc wrt bug 153766
+
+  03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> emboss-3.0.0-r1.ebuild:
+  Added ~sparc to emboss-3 for embassy-phylip-3.6b.
+
+  02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> emboss-4.0.0.ebuild=
:
+  Added to x86.
+
+  18 Aug 2006; Jason Wever <weeve@gentoo.org> emboss-4.0.0.ebuild:
+  Added ~sparc keyword wrt bug #144241.
+
+*emboss-4.0.0 (21 Jul 2006)
+
+  21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> +emboss-4.0.0.ebuil=
d:
+  New upstream version. See change log:
+  "http://emboss.sourceforge.net/developers/changelog.html".
+
+  20 Apr 2006; Olivier Fisette <ribosome@gentoo.org> -emboss-3.0.0.ebuil=
d:
+  Removed old revision.
+
+  08 Apr 2006; Simon Stelling <blubb@gentoo.org> emboss-3.0.0-r1.ebuild:
+  stable on amd64
+
+  22 Feb 2006; Fabian Groffen <grobian@gentoo.org> ChangeLog:
+  Marked ppc-macos stable (bug #123332)
+
+  22 Feb 2006; <nixnut@gentoo.org> emboss-3.0.0-r1.ebuild:
+  Stable on ppc. bug 123332
+
+  21 Feb 2006; Markus Rothe <corsair@gentoo.org> emboss-3.0.0-r1.ebuild:
+  Stable on ppc64; bug #123332
+
+  20 Feb 2006; Joshua Jackson <tsunam@gentoo.org> emboss-3.0.0-r1.ebuild=
:
+  Stable on x86; bug #123332
+
+  19 Feb 2006; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0-r1.ebu=
ild:
+  Block old versions of pscan to avoid file collisions (see bug #116236)=
.
+
+  23 Jan 2006; Olivier Fisette <ribosome@gentoo.org> +files/README.Gento=
o:
+  Added missing README file (fixes bug #120071).
+
+*emboss-3.0.0-r1 (21 Jan 2006)
+
+  21 Jan 2006; Olivier Fisette <ribosome@gentoo.org>
+  +emboss-3.0.0-r1.ebuild:
+  Install codons and restriction enzyme equivalence files in alternative
+  directories. This avoids file collisions on case insensitive filesyste=
ms
+  (see bug #115446), allows the installation of an updated enzyme protot=
ypes
+  file that will give more consistent results (see bug #118832).
+
+  14 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>; emboss-3.0.0.ebui=
ld:
+  Add modular X dependencies.
+
+  19 Nov 2005; Simon Stelling <blubb@gentoo.org> emboss-3.0.0.ebuild:
+  stable on amd64
+
+  04 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -emboss-2.10.0.ebui=
ld:
+  Removed obsolete version.
+
+  03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0.ebuild=
:
+  Stable on ppc-macos (with j4rg0n's permission, bug #102420).
+
+  02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> emboss-3.0.0.ebuil=
d:
+  Stable on ppc.
+
+  24 Sep 2005; Markus Rothe <corsair@gentoo.org> emboss-3.0.0.ebuild:
+  Stable on ppc64
+
+  21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0.ebuild=
:
+  Added to x86.
+
+  04 Sep 2005; Simon Stelling <blubb@gentoo.org> emboss-3.0.0.ebuild:
+  added ~amd64 keyword
+
+  13 Aug 2005; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0.ebuild=
,
+  emboss-2.10.0.ebuild:
+  Fixed Prosite dependency.
+
+*emboss-3.0.0 (06 Aug 2005)
+
+  06 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +emboss-3.0.0.ebuil=
d:
+  New version.
+
+  28 Jul 2005; Olivier Fisette <ribosome@gentoo.org> -emboss-2.9.0.ebuil=
d:
+  Removed old version.
+
+  25 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org> emboss-2.10.0.ebuild:
+  Stable ppc-macos
+
+  24 Jun 2005; Joseph Jezak <josejx@gentoo.org> emboss-2.10.0.ebuild:
+  Marked ppc stable for bug #96819.
+
+  19 Jun 2005; Markus Rothe <corsair@gentoo.org> emboss-2.10.0.ebuild:
+  Stable on ppc64
+
+  13 May 2005; Olivier Fisette <ribosome@gentoo.org> emboss-2.10.0.ebuil=
d:
+  Added to x86.
+
+  02 May 2005; Omkhar Arasaratnam <omkhar@gentoo.org> emboss-2.10.0.ebui=
ld:
+  Added ~ppc64
+
+  02 May 2005; Michael Hanselmann <hansmi@gentoo.org> emboss-2.9.0.ebuil=
d:
+  Stable on ppc.
+
+*emboss-2.10.0 (22 Mar 2005)
+
+  22 Mar 2005; Olivier Fisette <ribosome@gentoo.org> +emboss-2.10.0.ebui=
ld:
+  New version.
+
+  22 Feb 2005; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild=
:
+  Added support for minimal build.
+
+  09 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> emboss-2.9.0.ebuild:
+  Stable ppc-macos
+
+  30 Jan 2005; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild=
:
+  Ebuild cleanup.
+
+  01 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> emboss-2.9.0.ebuild:
+  Unstable ppc-macos.
+
+*emboss-2.9.0 (23 Dec 2004)
+
+  23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+  +files/22emboss-r1, +emboss-2.9.0.ebuild:
+  Moved from app-sci/emboss to sci-biology/emboss.
+
+  31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild=
,
+  -emboss-2.8.0-r3.ebuild:
+  Removed old version. Added 2.9.0 to x86.
+
+  10 Aug 2004; Olivier Fisette <ribosome@gentoo.org>
+  emboss-2.8.0-r3.ebuild:
+  Added to x86.
+  emboss-2.8.0-r2.ebuild:
+  Removed obsolete ebuild.
+
+  21 Jul 2004; David Holm <dholm@gentoo.org> emboss-2.9.0.ebuild:
+  Added to ~ppc.
+
+  20 Jul 2004; Olivier Fisette <ribosome@gentoo.org>
+  emboss-2.8.0-r3.ebuild, emboss-2.9.0.ebuild:
+  Removed icc support since no patching is needed.
+
+  19 Jul 2004; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild=
:
+  Version bump. Changed the configuration and install steps a bit to
+  reflect the fact that header files are now installed automatically.
+
+  14 Jul 2004; Olivier Fisette <ribosome@gentoo.org>
+  emboss-2.8.0-r3.ebuild: Modified configuration step to make the X and =
png
+  USE flags independent; Added support for icc; Added primer3 and clusta=
lw
+  to the dependencies since some EMBOSS programs won't work without them=
;
+  Added support for the biological databases aaindex, cutg, prints, pros=
ite,
+  rebase and transfac, which are needed for many EMBOSS programs (the da=
tabases
+  are PDEPENDencies since they all must be indexed with an EMBOSS progra=
m before
+  use) (this database support is optional); Added header files installat=
ion for
+  EMBOSS development.
+  emboss-2.8.0-r2.ebuild: Added to x86.
+  emboss-2.8.0-r1.ebuild, emboss-2.8.0.ebuild, emboss-2.7.1.ebuild: Remo=
ved files.
+  metadata.xml: Added long description; Set myself as maintainer.
+
+  02 Jun 2004; Aron Griffis <agriffis@gentoo.org> emboss-2.8.0-r1.ebuild=
,
+  emboss-2.8.0-r2.ebuild:
+  Fix use invocation
+
+  12 May 2004; David Holm <dholm@gentoo.org> emboss-2.8.0-r2.ebuild:
+  Added to ~ppc.
+
+*emboss-2.8.0-r2 (11 May 2004)
+
+  11 May 2004; Patrick Kursawe <phosphan@gentoo.org> emboss-2.8.0-r2.ebu=
ild,
+  files/22emboss-r1:
+  Adjusted value of PLPLOT_LIB, see bug #50176
+
+*emboss-2.8.0-r1 (30 Jan 2004)
+
+  30 Jan 2004; Stephen Diener <sediener@gentoo.org> emboss-2.8.0-r1.ebui=
ld:
+  Modified to use X and png properly for servers
+
+  28 Jan 2004; Stephen Diener <sediener@gentoo.org> emboss-2.8.0.ebuild:
+  Modified 2.8.0 ebuild to require X not just USE it.
+
+*emboss-2.8.0 (13 Dec 2003)
+
+  13 Dec 2003; Stephen Diener <sediener@gentoo.org> emboss-2.7.1.ebuild,
+  emboss-2.8.0.ebuild:
+  Version bump...
+
+  20 Oct 2003; George Shapovalov <george@gentoo.org> metdata.xml :
+  added metadata.xml, marked ebuild stable
+
+*emboss-2.7.1 (03 Sep 2003)
+
+  03 Sep 2003; <sediener@gentoo.org> emboss-2.7.1.ebuild:
+  Initial ebuild
+

diff --git a/sci-biology/emboss/emboss-6.3.1_p4.ebuild b/sci-biology/embo=
ss/emboss-6.3.1_p4.ebuild
new file mode 100644
index 0000000..e235c73
--- /dev/null
+++ b/sci-biology/emboss/emboss-6.3.1_p4.ebuild
@@ -0,0 +1,116 @@
+# 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_p4.eb=
uild,v 1.2 2011/03/09 16:29:05 jlec Exp $
+
+EAPI=3D"4"
+
+inherit autotools eutils
+
+MY_PATCH=3D"4"
+
+DESCRIPTION=3D"The European Molecular Biology Open Software Suite - A se=
quence analysis package"
+HOMEPAGE=3D"http://emboss.sourceforge.net/"
+SRC_URI=3D"
+	ftp://${PN}.open-bio.org/pub/EMBOSS/EMBOSS-${PV/_p${MY_PATCH}}.tar.gz
+	ftp://${PN}.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-${MY_PATCH}.g=
z -> ${P}.patch.gz"
+
+LICENSE=3D"GPL-2 LGPL-2"
+SLOT=3D"0"
+KEYWORDS=3D"~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-=
macos"
+IUSE=3D"doc +largefile minimal mysql pdf png postgres static-libs X"
+
+DEPEND=3D"
+	dev-libs/expat
+	dev-libs/libpcre:3
+	sci-libs/plplot
+	sys-libs/zlib
+	mysql? ( dev-db/mysql )
+	pdf? ( media-libs/libharu )
+	png? (
+		sys-libs/zlib
+		media-libs/libpng
+		media-libs/gd
+		)
+	postgres? ( dev-db/postgresql-base )
+	!minimal? (
+		sci-biology/primer3
+		sci-biology/clustalw
+		)
+	X? ( x11-libs/libXt )"
+RDEPEND=3D"${DEPEND}
+	!sys-devel/cons"
+PDEPEND=3D"
+	!minimal? (
+		sci-biology/aaindex
+		sci-biology/cutg
+		sci-biology/prints
+		sci-biology/prosite
+		sci-biology/rebase
+		sci-biology/transfac
+		)"
+
+S=3D"${WORKDIR}/EMBOSS-${PV/_p${MY_PATCH}}"
+
+src_prepare() {
+	epatch "${WORKDIR}"/${P}.patch
+	epatch \
+		"${FILESDIR}"/${PV}-unbundle-libs.patch
+	eautoreconf
+}
+
+src_configure() {
+	econf \
+		$(use_with X x) \
+		$(use_with png pngdriver "${EPREFIX}/usr") \
+		$(use_with doc docroot "${EPREFIX}/usr") \
+		$(use_with pdf hpdf "${EPREFIX}/usr") \
+		$(use_with mysql mysql "${EPREFIX}/usr/bin/mysql_config") \
+		$(use_with postgres postgresql "${EPREFIX}/usr/bin/pg_config") \
+		$(use_enable amd64 64) \
+		$(use_enable largefile large) \
+		$(use_enable static-libs static) \
+		--without-java \
+		--enable-systemlibs \
+		--includedir=3D"${ED}/usr/include/emboss"
+}
+
+src_install() {
+	einstall || die "Failed to install program files."
+
+	dodoc AUTHORS ChangeLog FAQ NEWS README THANKS
+	sed "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > READ=
ME.Gentoo && \
+	dodoc README.Gentoo
+
+	# Install env file for setting libplplot and acd files path.
+	cat <<- EOF > 22emboss
+		# plplot libs dir
+		PLPLOT_LIB=3D"${EPREFIX}/usr/share/EMBOSS/"
+		# ACD files location
+		EMBOSS_ACDROOT=3D"${EPREFIX}/usr/share/EMBOSS/acd"
+	EOF
+	doenvd 22emboss
+
+	# Symlink preinstalled docs to "/usr/share/doc".
+	dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${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 avo=
id
+	# user confusion and file collisions on case-insensitive file systems (=
see
+	# bug #115446). This change is documented in "README.Gentoo".
+	mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
+			die "Failed to move CODON directory."
+
+	# Move the provided restriction enzyme prototypes file to a different n=
ame.
+	# This avoids file collisions with versions of rebase that install thei=
r
+	# own enzyme prototypes file (see bug #118832).
+	mv "${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_p4.patch b/sci-biology/emboss=
/files/6.3.1_p4.patch
new file mode 100644
index 0000000..5e46374
--- /dev/null
+++ b/sci-biology/emboss/files/6.3.1_p4.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 =3D -I m4
+=20
+ AUTOMAKE_OPTIONS =3D gnits
+=20
+-SUBDIRS =3D plplot ajax nucleus emboss test doc jemboss
++if !ESYSTEMLIBS
++EXTRA_DIRS =3D plplot
++endif
++
++if GJEMBOSS
++JEMBOSS_DIR =3D jemboss
++endif
++
++SUBDIRS =3D $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR)
++DIST_SUBDIRS =3D $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_D=
IR)
+=20
+ # AJAX_FIXED_ROOT =3D \"`pwd`/emboss/acd\"
+=20
+ # files with nonstandard names in this directory
+-EXTRA_DIST =3D COMPAT LICENSE KNOWN_BUGS ONEWS PROBLEMS FAQ ChangeLog d=
epcomp ltmain.sh
++EXTRA_DIST =3D COMPAT KNOWN_BUGS ONEWS PROBLEMS FAQ ChangeLog depcomp l=
tmain.sh
+=20
+ # 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, inclus=
ion 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 =3D expat zlib
++EXTRA_DIRS =3D pcre expat zlib
+ endif
+=20
+-SUBDIRS =3D pcre $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
++SUBDIRS =3D $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
+diff --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am
+index 02bcaa7..368ddfe 100644
+--- a/ajax/acd/Makefile.am
++++ b/ajax/acd/Makefile.am
+@@ -13,10 +13,13 @@ CYGWIN_LDACD =3D -L../../plplot -L../pcre -L../expat=
 -L../zlib -L../core \
+ endif
+=20
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES =3D -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
++EXTRA_INCLUDES =3D -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib=
 \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
++else
++EXTRA_INCLUDES =3D $(PLPLOT_CFLAGS)
+ endif
+=20
+-INCLUDES =3D -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
++INCLUDES =3D  \
+ $(EXTRA_INCLUDES) \
+ -I$(top_srcdir)/ajax/core \
+ -I$(top_srcdir)/ajax/graphics \
+@@ -38,3 +41,4 @@ LINKFLAGS =3D $(VERS_INF)
+ endif
+=20
+ libacd_la_LDFLAGS =3D $(LINKFLAGS)
++libacd_la_LIBADD =3D ../core/libajax.la ../graphics/libajaxg.la ../ajax=
db/libajaxdb.la
+diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am
+index da57727..857ca5f 100644
+--- a/ajax/ajaxdb/Makefile.am
++++ b/ajax/ajaxdb/Makefile.am
+@@ -13,11 +13,12 @@ CYGWIN_LDAJAXDB =3D -L../../plplot -L../pcre -L../ex=
pat -L../zlib -L../core \
+ endif
+=20
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES =3D -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
++EXTRA_INCLUDES =3D -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib=
 \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
+ endif
+=20
+=20
+-INCLUDES =3D -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
++INCLUDES =3D \
+ $(EXTRA_INCLUDES) \
+ -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/ensembl
+=20
+@@ -37,3 +38,4 @@ LINKFLAGS =3D $(VERS_INF)
+ endif
+=20
+ libajaxdb_la_LDFLAGS =3D $(LINKFLAGS)
++libajaxdb_la_LIBADD =3D ../core/libajax.la ../ensembl/libensembl.la
+diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am
+index af27cb0..8fa4a3a 100644
+--- a/ajax/core/Makefile.am
++++ b/ajax/core/Makefile.am
+@@ -12,13 +12,18 @@ CYGWIN_LDAJAX =3D -L../../plplot -L../expat -L../pcr=
e -L../zlib \
+ endif
+=20
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES =3D -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
++EXTRA_INCLUDES =3D -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib=
 \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre=20
++else
++EXTRA_LIBS =3D -lexpat -lpcre
+ endif
+=20
++EXTRA_DIST =3D ajax-pcre-config.h.in
++DISTCLEAN =3D ajax-pcre-config.h
+=20
+ INCLUDES =3D -DAJAX_FIXED_ROOT=3D$(AJAX_FIXED_ROOT) \
+ -DAJAX_SYSTEM=3D"$(AJAX_SYSTEM)" -DPREFIX=3D\"$(prefix)\" \
+--I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre $(EXTRA_INCLUDES)
++$(EXTRA_INCLUDES) $(POSTGRESQL_CFLAGS) $(MYSQL_CFLAGS)
+=20
+ AJAXSRC =3D 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 ajseq=
write.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 =3D $(VERS_INF)
+ endif
+=20
+ libajax_la_LDFLAGS =3D $(LINKFLAGS)
++libajax_la_LIBADD =3D $(EXTRA_LIBS) $(POSTGRESQL_LDFLAGS) $(MYSQL_LDFLA=
GS)
+diff --git a/ajax/core/ajax-pcre-config.h.in b/ajax/core/ajax-pcre-confi=
g.h.in
+new file mode 100644
+index 0000000..b09e4e6
+--- /dev/null
++++ b/ajax/core/ajax-pcre-config.h.in
+@@ -0,0 +1 @@
++@DEFINE_USE_SYSTEM_PCRE@ AJAX_USE_SYSTEM_PCRE
+diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h
+index 06793be..659f462 100644
+--- a/ajax/core/ajreg.h
++++ b/ajax/core/ajreg.h
+@@ -16,9 +16,14 @@ extern "C"
+ #define ajreg_h
+=20
+ #include "ajax.h"
++#include "ajax-pcre-config.h"
++#ifndef AJAX_USE_SYSTEM_PCRE
+ #include "pcre_config.h"
+ #include "pcre_internal.h"
+ #include "pcreposix.h"
++#else
++#include <pcre.h>
++#endif
+=20
+ #define AJREG_OVECSIZE 30
+=20
+@@ -41,7 +46,11 @@ extern "C"
+ ***********************************************************************=
*******/
+=20
+ typedef struct AjSRegexp {
++#ifndef AJAX_USE_SYSTEM_PCRE
+     real_pcre *pcre;
++#else
++    pcre *pcre;
++#endif
+     pcre_extra *extra;
+     int *ovector;
+     const char* orig;
+diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am
+index ca33a84..87e51bd 100644
+--- a/ajax/ensembl/Makefile.am
++++ b/ajax/ensembl/Makefile.am
+@@ -10,12 +10,13 @@ CYGWIN_LDENSEMBL =3D -L../../plplot -L../expat -L../=
pcre -L../core -lajax -leplplo
+ endif
+=20
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES =3D -I$(top_srcdir)/ajax/expat
++EXTRA_INCLUDES =3D -I$(top_srcdir)/ajax/expat \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre=20
+ endif
+=20
+=20
+-INCLUDES =3D -I$(top_srcdir)/plplot $(EXTRA_INCLUDES) \
+--I$(top_srcdir)/ajax/pcre -I$(top_srcdir)/ajax/core
++INCLUDES =3D $(EXTRA_INCLUDES) \
++-I$(top_srcdir)/ajax/core
+=20
+ ENSEMBLSRC =3D ensanalysis.c ensassembly.c ensassemblyexception.c \
+ ensassemblymapper.c ensattribute.c ensbaseadaptor.c enscache.c \
+@@ -56,3 +57,4 @@ LINKFLAGS =3D $(VERS_INF)
+ endif
+=20
+ libensembl_la_LDFLAGS =3D $(LINKFLAGS)
++libensembl_la_LIBADD =3D ../core/libajax.la
+diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am
+index ab45afc..f61c605 100644
+--- a/ajax/graphics/Makefile.am
++++ b/ajax/graphics/Makefile.am
+@@ -10,11 +10,15 @@ CYGWIN_LDAJAXG =3D -L../../plplot -L../expat -L../pc=
re -L../core -lajax -leplplot
+ endif
+=20
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES =3D -I$(top_srcdir)/ajax/expat
++EXTRA_INCLUDES =3D -I$(top_srcdir)/ajax/expat \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
++else
++EXTRA_INCLUDES =3D $(PLPLOT_CFLAGS) -DUSE_PLXSFNAM_SHIM
++EXTRA_LIBS =3D $(PLPLOT_LIBS)
+ endif
+=20
+=20
+-INCLUDES =3D -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
++INCLUDES =3D \
+ $(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core
+=20
+ AJAXGSRC =3D ajgraph.c ajhist.c
+@@ -32,3 +36,4 @@ LINKFLAGS =3D $(VERS_INF)
+ endif
+=20
+ libajaxg_la_LDFLAGS =3D $(LINKFLAGS)
++libajaxg_la_LIBADD =3D ../core/libajax.la $(EXTRA_LIBS)
+diff --git a/ajax/graphics/ajgraph.c b/ajax/graphics/ajgraph.c
+index 25e75e4..60f2743 100644
+--- a/ajax/graphics/ajgraph.c
++++ b/ajax/graphics/ajgraph.c
+@@ -34,10 +34,8 @@
+ #include <float.h>
+ #define AZ 28
+=20
+-
+ #include "plplotP.h"
+=20
+-
+ static void     GraphArray(ajuint numofpoints,
+ 			   float *x, float *y);
+ static void     GraphArrayGaps(ajuint numofpoints,
+@@ -1049,13 +1047,26 @@ static void GraphDefCharSize(float size)
+ ** @@
+ ***********************************************************************=
*******/
+=20
++#define _GNU_SOURCE
++#include <stdio.h>
++
+ static void GraphSetName(const AjPGraph thys,
+ 			 const AjPStr txt, const char *ext)
+ {
+     if(!thys->ready)
+     {
++#ifdef USE_PLXSFNAM_SHIM
++        char *fullname;
++#endif
+         ajDebug("=3Dg=3D plxsfnam ('%S', '%s')\n", txt, ext);
++#ifdef USE_PLXSFNAM_SHIM
++        fullname =3D asprintf(fullname,"%s%s", ajStrGetPtr(txt), ext);
++        ajDebug("=3Dg=3D plsfnam ('%S') instead\n", fullname);
++        plsfnam(fullname);
++        free(fullname);
++#else
+         plxsfnam(ajStrGetPtr(txt), ext);
++#endif
+         ajStrAssignS(&graphBasename, txt);
+         ajStrAssignC(&graphExtension, ext);
+         if(ajStrGetCharFirst(graphExtension) =3D=3D '.')
+diff --git a/configure.in b/configure.in
+index ddb4f81..3f4fe5e 100644
+--- a/configure.in
++++ b/configure.in
+@@ -235,15 +235,6 @@ AC_PROG_INSTALL
+ AC_PROG_LN_S
+ AC_PROG_MAKE_SET
+=20
+-dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+-if test "${with_x}" !=3D "no" ; then
+-if test "`uname -a | grep Darwin`"; then
+-OSXX=3D`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'`
+-if test ${OSXX} '>' '10.4'; then
+-CFLAGS=3D"$CFLAGS -I/usr/X11/include -L/usr/X11/lib"
+-fi
+-fi
+-fi
+=20
+ # 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])
+=20
+-if test "${with_x}" !=3D "no" ; then
+-LF_EMBOSS_PATH_XLIB
+-fi
+=20
+ dnl Library checks
+ AC_CHECK_LIB(c, socket, LIBS=3D"$LIBS" , LIBS=3D"$LIBS -lsocket")
+@@ -316,14 +304,16 @@ CHECK_PNGDRIVER
+ CHECK_AUTH
+ CHECK_AMD64
+=20
++AM_CONDITIONAL(GJEMBOSS, test "$JAVA_OK" =3D "yes")
++
+ AX_LIB_MYSQL
+ AX_LIB_POSTGRESQL
+=20
+ CFLAGS=3D"$CFLAGS $MYSQL_CFLAGS"
+ LDFLAGS=3D"$LDFLAGS $MYSQL_LDFLAGS"
+=20
+-CFLAGS=3D"$CFLAGS $POSTGRESQL_CFLAGS"
+-LDFLAGS=3D"$LDFLAGS $POSTGRESQL_LDFLAGS"
++CFLAGS=3D"$POSTGRESQL_CFLAGS $CFLAGS"
++LDFLAGS=3D"$POSTGRESQL_LDFLAGS $LDFLAGS"
+=20
+=20
+ dnl Check for 'ant' for packaging Jemboss and export result
+@@ -443,13 +433,36 @@ fi
+=20
+ dnl Test if --enable-systemlibs given
+ have_systemlibs=3Dno
++DEFINE_USE_SYSTEM_PCRE=3D"#undef"
+ AC_ARG_ENABLE(systemlibs,
+    AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles]=
))
++AC_MSG_CHECKING(for systemlib usage)
+ if test "${enable_systemlibs}" =3D "yes" ; then
+     have_systemlibs=3Dyes
++    DEFINE_USE_SYSTEM_PCRE=3D"#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}" !=3D "no" ; then
++    if test "`uname -a | grep Darwin`"; then
++    OSXX=3D`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'`
++    if test ${OSXX} '>' '10.4'; then
++    CFLAGS=3D"$CFLAGS -I/usr/X11/include -L/usr/X11/lib"
++    fi
++    fi
++    fi
++    if test "${with_x}" !=3D "no" ; then
++    LF_EMBOSS_PATH_XLIB
++    fi
++     AC_MSG_NOTICE(USING bundled LIBS)
+ fi         =20
+ AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" =3D "yes")
+ AC_SUBST(ESYSTEMLIBS)
++AC_SUBST(DEFINE_USE_SYSTEM_PCRE)
++AC_SUBST(PLPLOT_CFLAGS)
++AC_SUBST(PLPLOT_LIBS)
+=20
+=20
+=20
+@@ -457,7 +470,6 @@ AC_SUBST(ESYSTEMLIBS)
+=20
+ 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
+=20
+=20
+ AC_OUTPUT([plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Ma=
kefile
++ajax/core/ajax-pcre-config.h
+ ajax/pcre/Makefile ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Mak=
efile
+ 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
+=20
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES =3D -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
++EXTRA_INCLUDES =3D -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib=
 \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
++else
++EXTRA_INCLUDES =3D $(PLPLOT_CFLAGS)
+ endif
+=20
+-INCLUDES =3D -I$(top_srcdir)/nucleus -I$(top_srcdir)/ajax/pcre \
++INCLUDES =3D -I$(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
+=20
+=20
+ aaindexextract_SOURCES =3D aaindexextract.c
+@@ -319,7 +322,7 @@ testplot_SOURCES =3D testplot.c
+ treetypedisplay_SOURCES =3D treetypedisplay.c
+=20
+ if !ESYSTEMLIBS
+-EXTRA_LDS =3D ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la
++EXTRA_LDS =3D ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la ../pl=
plot/libeplplot.la ../ajax/pcre/libepcre.la
+ endif
+=20
+=20
+@@ -327,7 +330,6 @@ LDADD =3D ../nucleus/libnucleus.la ../ajax/acd/libac=
d.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)
+=20
+ pkgdata_DATA =3D 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
++# =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D
++#       http://www.gnu.org/software/autoconf-archive/ax_lib_mysql.html
++# =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D
+ #
+ # 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 o=
f
++#   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 th=
ere
++#   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_confi=
g
++#   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-point=
ers,
+-#                  which prevents gdb from displaying stack traces.
+-#                  Changed mysql_config --cflags to mysql_config --incl=
ude
++#   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 noti=
ce
++#   and this notice are preserved. This file is offered as-is, without =
any
++#   warranty.
++
++#serial 12
+=20
+ AC_DEFUN([AX_LIB_MYSQL],
+ [
+     AC_ARG_WITH([mysql],
+-        [AS_HELP_STRING([--with-mysql=3D@<:@ARG@:>@],
++        AS_HELP_STRING([--with-mysql=3D@<:@ARG@:>@],
+             [use MySQL client library @<:@default=3Dyes@:>@, optionally=
 specify path to mysql_config]
+-        )],
++        ),
+         [
+         if test "$withval" =3D "no"; then
+             want_mysql=3D"no"
+@@ -66,19 +63,20 @@ AC_DEFUN([AX_LIB_MYSQL],
+         ],
+         [want_mysql=3D"yes"]
+     )
++    AC_ARG_VAR([MYSQL_CONFIG], [Full path to mysql_config program])
+=20
+     MYSQL_CFLAGS=3D""
+     MYSQL_LDFLAGS=3D""
+     MYSQL_VERSION=3D""
+=20
+     dnl
+-    dnl Check MySQL libraries (libpq)
++    dnl Check MySQL libraries
+     dnl
+=20
+     if test "$want_mysql" =3D "yes"; then
+=20
+-        if test -z "$MYSQL_CONFIG" -o test; then
+-            AC_PATH_PROG([MYSQL_CONFIG], [mysql_config], [no])
++        if test -z "$MYSQL_CONFIG" ; then
++            AC_PATH_PROGS([MYSQL_CONFIG], [mysql_config mysql_config5],=
 [no])
+         fi
+=20
+         if test "$MYSQL_CONFIG" !=3D "no"; then
+@@ -90,35 +88,8 @@ dnl         MYSQL_CFLAGS=3D"`$MYSQL_CONFIG --cflags`"
+=20
+             MYSQL_VERSION=3D`$MYSQL_CONFIG --version`
+=20
+-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=3D$CFLAGS
+-	    EMBLDFLAGS=3D$LDFLAGS
+-	    CFLAGS=3D$MYSQL_CFLAGS
+-	    LDFLAGS=3D$MYSQL_LDFLAGS
+-
+-            AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <stdio.h>
+-                                              #include "mysql.h"]],
+-					    [[mysql_info(NULL)]])],
+-			   [havemysql=3Dyes],
+-			   [havemysql=3Dno])
+-
+-	    CFLAGS=3D$EMBCFLAGS
+-	    LDFLAGS=3D$EMBLDFLAGS
+-
+-            if test "$havemysql" =3D yes; then
+-                AC_DEFINE([HAVE_MYSQL], [1],
+-                    [Define to 1 if MySQL libraries are available])
+-                found_mysql=3D"yes"
+-                AC_MSG_RESULT([yes])
+-            else
+-	        MYSQL_CFLAGS=3D""
+-	        MYSQL_LDFLAGS=3D""
+-                found_mysql=3D"no"
+-                AC_MSG_RESULT([no])
+-            fi
++            found_mysql=3D"yes"
++            AC_MSG_RESULT([yes])
+         else
+             found_mysql=3D"no"
+             AC_MSG_RESULT([no])
+@@ -170,6 +141,11 @@ dnl not be installed
+         fi
+     fi
+=20
++    if test "$found_mysql" =3D "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 =3D -L../plplot -L../ajax/pcre -L../ajax=
/expat -L../ajax/zlib \
+ -lezlib -leplplot
+ else
+ if !ESYSTEMLIBS
+-EXTRA_INCLUDES =3D -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
++EXTRA_INCLUDES =3D -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib=
 \
++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
++else
++EXTRA_INCLUDES =3D $(PLPLOT_CFLAGS)
+ endif
+ endif
+=20
+=20
+-INCLUDES =3D -I$(top_srcdir)/plplot $(X_CFLAGS) -I$(srcdir)/ \
+-	-I$(top_srcdir)/ajax -I$(top_srcdir)/ajax/pcre \
++INCLUDES =3D $(X_CFLAGS) -I$(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 =3D  $(VERS_INF)
+ endif
+=20
+ libnucleus_la_LDFLAGS =3D  $(LINKFLAGS)
++libnucleus_la_LIBADD =3D ../ajax/core/libajax.la ../ajax/graphics/libaj=
axg.la ../ajax/acd/libacd.la

diff --git a/sci-biology/emboss/files/emboss-README.Gentoo-2 b/sci-biolog=
y/emboss/files/emboss-README.Gentoo-2
new file mode 100644
index 0000000..72fa366
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-README.Gentoo-2
@@ -0,0 +1,34 @@
+Administrating EMBOSS on Gentoo systems
+=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
+
+
+Codon data files location
+-------------------------
+
+The codon data files that are distributed with EMBOSS are installed in t=
he
+``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the u=
sual
+``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusio=
n 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 t=
he
+root filesystem is case insensitive. If you do not have the CUTG databas=
e
+installed and want to use the codon files distributed with EMBOSS, you c=
an
+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 inst=
alled
+as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the u=
sual
+``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 f=
ile
+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/metadat=
a.xml
new file mode 100644
index 0000000..747e4ab
--- /dev/null
+++ b/sci-biology/emboss/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version=3D"1.0" encoding=3D"UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-biology</herd>
+	<longdescription>
+		EMBOSS is "The European Molecular Biology Open Software Suite".
+		EMBOSS is a free Open Source software analysis package specially
+		developed for the needs of the molecular biology (e.g. EMBnet) user
+		community. The software automatically copes with data in a variety
+		of formats and even allows transparent retrieval of sequence data
+		from the web. Also, as extensive libraries are provided with the
+		package, it is a platform to allow other scientists to develop and
+		release software in true open source spirit. EMBOSS also integrates
+		a range of currently available packages and tools for sequence
+		analysis into a seamless whole. EMBOSS breaks the historical trend
+		towards commercial software packages.
+	</longdescription>
+<use>
+  <flag name=3D'largefile'>Support for large files</flag>
+</use>
+</pkgmetadata>