From: Olivier Fisette Date: Thu, 23 Dec 2004 21:17:14 +0000 (+0000) Subject: Moving to sci-biology/aaindex X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=e40ee2eca5eb5d402eb4bea92814b2792cea132c;p=gentoo.git Moving to sci-biology/aaindex --- diff --git a/app-sci/aaindex/ChangeLog b/app-sci/aaindex/ChangeLog deleted file mode 100644 index 3f2b7e720a2f..000000000000 --- 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 aaindex-6.0.ebuild: - Keyworded ~ppc-macos. - - 10 Aug 2004; Olivier Fisette aaindex-6.0.ebuild: - Added to x86. - - 26 Jun 2004; David Holm aaindex-6.0.ebuild: - Added to ~ppc. - -*aaindex-6.0 (24 Jun 2004) - - 24 Jun 2004; Olivier Fisette - aaindex-6.0.ebuild, metadata.xml : - Initial import. Ebuild submitted by Olivier Fisette . - Reference: Gentoo Bugzilla, bug #54319 - diff --git a/app-sci/aaindex/Manifest b/app-sci/aaindex/Manifest deleted file mode 100644 index 08f93845ec12..000000000000 --- 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 index b2d1e039ceb4..000000000000 --- 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 index c864f17ccc82..000000000000 --- 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 index 9845c316a061..000000000000 --- a/app-sci/aaindex/metadata.xml +++ /dev/null @@ -1,26 +0,0 @@ - - - - - ribosome@gentoo.org - Olivier Fisette - - sci - - 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. - -