--- /dev/null
+# ChangeLog for app-sci/emboss
+# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.1 2004/12/23 22:51:48 ribosome Exp $
+
+*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 clustalw
+ to the dependencies since some EMBOSS programs won't work without them;
+ Added support for the biological databases aaindex, cutg, prints, prosite,
+ rebase and transfac, which are needed for many EMBOSS programs (the databases
+ are PDEPENDencies since they all must be indexed with an EMBOSS program before
+ use) (this database support is optional); Added header files installation 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: Removed 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.ebuild,
+ 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.ebuild:
+ 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
+
--- /dev/null
+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-2.9.0.ebuild,v 1.1 2004/12/23 22:51:48 ribosome Exp $
+
+DESCRIPTION="The European Molecular Biology Open Software Suite: a sequence analysis package."
+HOMEPAGE="http://emboss.sourceforge.net/"
+SRC_URI="ftp://ftp.uk.embnet.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz"
+LICENSE="GPL-2 LGPL-2"
+
+SLOT="0"
+KEYWORDS="x86 ~ppc"
+IUSE="X png no-biodata"
+
+DEPEND="X? ( virtual/x11 )
+ png? (
+ sys-libs/zlib
+ media-libs/libpng
+ >=media-libs/gd-1.8
+ )
+ sci-biology/primer3
+ sci-biology/clustalw"
+
+PDEPEND="!no-biodata? (
+ sci-biology/aaindex
+ sci-biology/cutg
+ sci-biology/prints
+ sci-biology/prosite
+ sci-biology/rebase
+ sci-biology/transfac
+ )"
+
+S=${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"
+
+ econf ${EXTRA_CONF} || die
+ # Do not install the JEMBOSS component (the --without-java configure option
+ # does not work). JEMBOSS will 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/' Makefile
+ emake || die
+}
+
+src_install() {
+ einstall || die
+ dodoc AUTHORS ChangeLog FAQ NEWS README THANKS
+
+ # Install env file for setting libplplot and acd files path.
+ insinto /etc/env.d
+ newins ${FILESDIR}/22emboss-r1 22emboss
+
+ # Symlink preinstalled docs to /usr/share/doc.
+ dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals
+ dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs
+ dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials
+}
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer>
+ <email>ribosome@gentoo.org</email>
+ <name>Olivier Fisette</name>
+ </maintainer>
+ <herd>sci</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>
+</pkgmetadata>
projects / gentoo.git / commitdiff