Moving to sci-biology/emboss

6 files changed, 0 insertions, 163 deletions

diff --git a/app-sci/emboss/ChangeLog b/app-sci/emboss/ChangeLog
deleted file mode 100644
index a09bff4dc2c0..000000000000
--- a/app-sci/emboss/ChangeLog
+++ /dev/null
@@ -1,73 +0,0 @@
-# ChangeLog for app-sci/emboss
-# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/emboss/ChangeLog,v 1.15 2004/11/01 01:28:06 ribosome Exp $
-
-  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
-
diff --git a/app-sci/emboss/Manifest b/app-sci/emboss/Manifest
deleted file mode 100644
index 87e3b32a9144..000000000000
--- a/app-sci/emboss/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-MD5 02e17352ecec7dabbaa1aab84769e746 emboss-2.9.0.ebuild 1779
-MD5 1b0826c48804a608a2bb548e7c27dc93 ChangeLog 2789
-MD5 6051afb1f26bf343082490327784b958 metadata.xml 1013
-MD5 68e42b6377bb0887a0aeac76cf530854 files/digest-emboss-2.9.0 66
-MD5 ef2dfa3d13837026f59c0cf5f04f67c5 files/22emboss-r1 110
diff --git a/app-sci/emboss/emboss-2.9.0.ebuild b/app-sci/emboss/emboss-2.9.0.ebuild
deleted file mode 100644
index 753a865f9576..000000000000
--- a/app-sci/emboss/emboss-2.9.0.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/emboss/emboss-2.9.0.ebuild,v 1.7 2004/12/23 21:29:30 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
-}
diff --git a/app-sci/emboss/files/22emboss-r1 b/app-sci/emboss/files/22emboss-r1
deleted file mode 100644
index 177643ced11f..000000000000
--- a/app-sci/emboss/files/22emboss-r1
+++ /dev/null
@@ -1,4 +0,0 @@
-# plplot libs dir
-PLPLOT_LIB="/usr/share/EMBOSS/"
-# ACD files location
-EMBOSS_ACDROOT="/usr/share/EMBOSS/acd"
diff --git a/app-sci/emboss/files/digest-emboss-2.9.0 b/app-sci/emboss/files/digest-emboss-2.9.0
deleted file mode 100644
index ab9c2bc595ca..000000000000
--- a/app-sci/emboss/files/digest-emboss-2.9.0
+++ /dev/null
@@ -1 +0,0 @@
-MD5 c6facfd1750e88a0c8b7bb7ac826d472 EMBOSS-2.9.0.tar.gz 14479274
diff --git a/app-sci/emboss/metadata.xml b/app-sci/emboss/metadata.xml
deleted file mode 100644
index ff86b6a3a444..000000000000
--- a/app-sci/emboss/metadata.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?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>