Initial import for app-sci/aaindex

6 files changed, 94 insertions, 0 deletions

diff --git a/app-sci/aaindex/ChangeLog b/app-sci/aaindex/ChangeLog
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+# ChangeLog for app-sci/aaindex
+# Copyright 2000-2004 Gentoo Technologies, Inc.; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/app-sci/aaindex/ChangeLog,v 1.1 2004/06/25 03:28:39 ribosome Exp $
+
+*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
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index 000000000000..c8d5af7729d1
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+++ b/app-sci/aaindex/Manifest
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+MD5 2368a4212b8549a98c16a0db59f1fbcf aaindex-6.0.ebuild 1436
+MD5 1790a3c55ed8b7f8d5b816def8faaf2e ChangeLog 451
+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
new file mode 100644
index 000000000000..5d8fd3cf87ec
--- /dev/null
+++ b/app-sci/aaindex/aaindex-6.0.ebuild
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+# Copyright 1999-2004 Gentoo Technologies, Inc.
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/app-sci/aaindex/aaindex-6.0.ebuild,v 1.1 2004/06/25 03:28:39 ribosome 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/${PN}/list_of_indices"
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE="no-emboss no-rawdb"
+
+S=${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
new file mode 100644
index 000000000000..c864f17ccc82
--- /dev/null
+++ b/app-sci/aaindex/files/digest-aaindex-6.0
@@ -0,0 +1,5 @@
+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
new file mode 100644
index 000000000000..9845c316a061
--- /dev/null
+++ b/app-sci/aaindex/metadata.xml
@@ -0,0 +1,26 @@
+<?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>
diff --git a/app-sci/cutg/Manifest b/app-sci/cutg/Manifest
new file mode 100644
index 000000000000..d825586fcdc2
--- /dev/null
+++ b/app-sci/cutg/Manifest
@@ -0,0 +1,4 @@
+MD5 255214763a6d541ef55959fed8c182bc cutg-141.0.ebuild 1122
+MD5 2fd652433bcdbcbd76d2328e5527e9f6 ChangeLog 443
+MD5 d14f29edef39d8d89b39a5787c3d141c metadata.xml 594
+MD5 4a2ff548dd1ae81fb6ae0e63b1966298 files/digest-cutg-141.0 63