Moving to sci-biology/aaindex

diff --git a/app-sci/aaindex/ChangeLog b/app-sci/aaindex/ChangeLog
deleted file mode 100644 (file)
index 3f2b7e7..0000000
--- a/app-sci/aaindex/ChangeLog
+++ /dev/null
@@ -1,20 +0,0 @@
-# ChangeLog for app-sci/aaindex
-# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/aaindex/ChangeLog,v 1.5 2004/11/03 02:47:42 j4rg0n Exp $
-
-  2 Nov 2004; Lina Pezzella <j4rg0n@gentoo.org> aaindex-6.0.ebuild:
-  Keyworded ~ppc-macos.
-
-  10 Aug 2004; Olivier Fisette <ribosome@gentoo.org> aaindex-6.0.ebuild:
-  Added to x86.
-
-  26 Jun 2004; David Holm <dholm@gentoo.org> aaindex-6.0.ebuild:
-  Added to ~ppc.
-
-*aaindex-6.0 (24 Jun 2004)
-
-  24 Jun 2004; Olivier Fisette <ribosome@gentoo.org>
-  aaindex-6.0.ebuild, metadata.xml :
-  Initial import.  Ebuild submitted by Olivier Fisette <ribosome@gentoo.org>.
-  Reference: Gentoo Bugzilla, bug #54319
-

diff --git a/app-sci/aaindex/Manifest b/app-sci/aaindex/Manifest
deleted file mode 100644 (file)
index 08f9384..0000000
--- a/app-sci/aaindex/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-MD5 7e5d46b17d8c21057a79e39196f8acf3 ChangeLog 707
-MD5 2c646aebfcfeb537ca42ac037069708a aaindex-6.0.ebuild 1441
-MD5 d508af45f2137bf67613eb18d9f6f831 metadata.xml 1310
-MD5 cd3e50367768bef809d98048504b43d6 files/digest-aaindex-6.0 278

diff --git a/app-sci/aaindex/aaindex-6.0.ebuild b/app-sci/aaindex/aaindex-6.0.ebuild
deleted file mode 100644 (file)
index b2d1e03..0000000
--- a/app-sci/aaindex/aaindex-6.0.ebuild
+++ /dev/null
@@ -1,44 +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/aaindex/aaindex-6.0.ebuild,v 1.5 2004/11/03 02:47:42 j4rg0n Exp $
-
-DESCRIPTION="Amino acid indices and similarity matrices"
-HOMEPAGE="http://www.genome.ad.jp/${PN}/"
-SRC_URI="ftp://ftp.genome.ad.jp/pub/db/genomenet/${PN}/${PN}.doc
-       ftp://ftp.genome.ad.jp/pub/db/genomenet/${PN}/${PN}1
-       ftp://ftp.genome.ad.jp/pub/db/genomenet/${PN}/${PN}2
-       ftp://ftp.genome.ad.jp/pub/db/genomenet/${PN}/list_of_matrices
-       ftp://ftp.genome.ad.jp/pub/db/genomenet/${PN}/list_of_indices"
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="x86 ~ppc ~ppc-macos"
-IUSE="no-emboss no-rawdb"
-
-S=${WORKDIR}
-
-src_unpack() {
-       einfo "No archive to unpack."
-}
-
-src_compile() {
-       # Index the database for use with emboss if emboss is installed and
-       # the user did not explicitly request not to index the database.
-       if [ -e /usr/bin/aaindexextract ] && ! use no-emboss; then
-               mkdir AAINDEX
-               einfo "Indexing AAindex for usage with EMBOSS."
-               EMBOSS_DATA=. aaindexextract -auto -infile ${DISTDIR}/${PN}1 || die \
-                       "Indexing AAindex failed."
-       fi
-}
-
-src_install() {
-       if ! use no-rawdb; then
-               insinto /usr/share/${PN}
-               doins ${DISTDIR}/{${PN}{1,2},list_of_{matrices,indices}}
-       fi
-       dodoc ${DISTDIR}/${PN}.doc
-       if [ -e /usr/bin/aaindexextract ] && ! use no-emboss; then
-               insinto /usr/share/EMBOSS/data/AAINDEX
-               doins AAINDEX/*
-       fi
-}

diff --git a/app-sci/aaindex/files/digest-aaindex-6.0 b/app-sci/aaindex/files/digest-aaindex-6.0
deleted file mode 100644 (file)
index c864f17..0000000
--- a/app-sci/aaindex/files/digest-aaindex-6.0
+++ /dev/null
@@ -1,5 +0,0 @@
-MD5 313ec8e18370195b58a95e6524c858ff aaindex.doc 6190
-MD5 90b5841a3d3c077b3e6b1ebb7781265b aaindex1 428020
-MD5 9ea0047f2727adf76285fc296d51594a aaindex2 195457
-MD5 74abb4c58caa1cb917b407cd6d05a18c list_of_matrices 6900
-MD5 4146e937362ee420ea32544ea2c8df2a list_of_indices 37549

diff --git a/app-sci/aaindex/metadata.xml b/app-sci/aaindex/metadata.xml
deleted file mode 100644 (file)
index 9845c31..0000000
--- a/app-sci/aaindex/metadata.xml
+++ /dev/null
@@ -1,26 +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>
-               Amino acid indices and similarity matrices maintained at Kyoto
-               University. An amino acid index is a set of 20 numerical values
-               representing any of the different physicochemical and biological
-               properties of amino acids.  The AAindex1 section of the Amino Acid
-               Index Database is a collection of published indices together with the
-               result of cluster analysis using the correlation coefficient as the
-               distance between two indices.  This section currently contains 494
-               indices. Another important feature of amino acids that can be
-               represented numerically is the similarity between amino acids.  Thus, a
-               similarity matrix, also called a mutation matrix, is a set of 210
-               numerical values, 20 diagonal and 20x19/2 off-diagonal elements, used
-               for sequence alignments and similarity searches.  The AAindex2 section
-               of the Amino Acid Index Database is a collection of published amino
-               acid mutation matrices together with the result of cluster analysis.
-               This section currently contains 83 matrices.
-       </longdescription>
-</pkgmetadata>