From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from <gentoo-commits+bounces-324190-garchives=archives.gentoo.org@lists.gentoo.org>) id 1Pxl7s-0001N9-8s for garchives@archives.gentoo.org; Thu, 10 Mar 2011 19:02:23 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id EC4D3E0539; Thu, 10 Mar 2011 19:00:21 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id 77EE3E0517 for <gentoo-commits@lists.gentoo.org>; Thu, 10 Mar 2011 19:00:21 +0000 (UTC) Received: from pelican.gentoo.org (unknown [66.219.59.40]) (using TLSv1 with cipher ADH-CAMELLIA256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 9934C1B40D2 for <gentoo-commits@lists.gentoo.org>; Thu, 10 Mar 2011 19:00:20 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id 0D7448006A for <gentoo-commits@lists.gentoo.org>; Thu, 10 Mar 2011 19:00:20 +0000 (UTC) From: "Justin Lecher" <jlec@gentoo.org> To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" <jlec@gentoo.org> Message-ID: <895a849ade4a8dc6d5e0d49d6c8d8b5556eeca05.jlec@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/files/, sci-biology/emboss/ X-VCS-Repository: proj/sci 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 X-VCS-Directories: sci-biology/emboss/files/ sci-biology/emboss/ X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: 895a849ade4a8dc6d5e0d49d6c8d8b5556eeca05 Date: Thu, 10 Mar 2011 19:00:20 +0000 (UTC) Precedence: bulk List-Post: <mailto:gentoo-commits@lists.gentoo.org> List-Help: <mailto:gentoo-commits+help@lists.gentoo.org> List-Unsubscribe: <mailto:gentoo-commits+unsubscribe@lists.gentoo.org> List-Subscribe: <mailto:gentoo-commits+subscribe@lists.gentoo.org> List-Id: Gentoo Linux mail <gentoo-commits.gentoo.org> X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: X-Archives-Hash: 54814968656f7c82660864031cbafd96 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>