Initial import.

Package-Manager: portage-2.0.51-r15

5 files changed, 95 insertions, 0 deletions

diff --git a/sci-biology/t-coffee/ChangeLog b/sci-biology/t-coffee/ChangeLog
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+# ChangeLog for sci-biology/t-coffee
+# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.1 2005/03/03 18:41:31 ribosome Exp $
+
+*t-coffee-2.03 (03 Mar 2005)
+
+  03 Mar 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+  +t-coffee-2.03.ebuild:
+  Initial import.
+
diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest
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index 000000000000..d1640782d1a9
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+++ b/sci-biology/t-coffee/Manifest
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+MD5 ba7eb142bfd24a0004f65c04bae8025e t-coffee-2.03.ebuild 1516
+MD5 72c8c9734d7d1d9d59c1be0f97d1d759 ChangeLog 357
+MD5 0bbfd32ca9864625c55ab6460dbbd963 metadata.xml 755
+MD5 733ccc786341ddaabbed48391bcdb961 files/digest-t-coffee-2.03 86
diff --git a/sci-biology/t-coffee/files/digest-t-coffee-2.03 b/sci-biology/t-coffee/files/digest-t-coffee-2.03
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index 000000000000..66af76629bc9
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+++ b/sci-biology/t-coffee/files/digest-t-coffee-2.03
@@ -0,0 +1 @@
+MD5 a86e2d83c17058b03be0170566d634f0 T-COFFEE_distribution_Version_2.03.tar.gz 864853
diff --git a/sci-biology/t-coffee/metadata.xml b/sci-biology/t-coffee/metadata.xml
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index 000000000000..a6dacf3d67e9
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+++ b/sci-biology/t-coffee/metadata.xml
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+<?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>
+		T-Coffee is a multiple sequence alignment package. Given a set of
+		sequences (Proteins or DNA), T-Coffee generates a multiple sequence
+		alignment. Version 2.00 and higher can mix sequences and structures.
+		T-Coffee allows the combination of a collection of multiple/pairwise,
+		global or local alignments into a single model. It also allows to
+		estimate the level of consistency of each position within the new
+		alignment with the rest of the alignments.
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/t-coffee/t-coffee-2.03.ebuild b/sci-biology/t-coffee/t-coffee-2.03.ebuild
new file mode 100644
index 000000000000..250facab04ef
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+++ b/sci-biology/t-coffee/t-coffee-2.03.ebuild
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+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/t-coffee-2.03.ebuild,v 1.1 2005/03/03 18:41:31 ribosome Exp $
+
+inherit toolchain-funcs
+
+DESCRIPTION="A multiple sequence alignment package"
+HOMEPAGE="http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html"
+SRC_URI="http://igs-server.cnrs-mrs.fr/~cnotred/Packages/T-COFFEE_distribution_Version_${PV}.tar.gz"
+LICENSE="t-coffee"
+
+RESTRICT="nomirror"
+
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+DEPEND="sci-biology/clustalw"
+
+TCDIR="${WORKDIR}/T-COFFEE_distribution_Version_${PV}"
+S=${TCDIR}/t_coffee_source
+
+src_unpack(){
+	unpack ${A}
+	cd ${S}
+	sed -i -e "s/CC	= cc/CC	= $(tc-getCC) ${CFLAGS}/" makefile || die || die
+	cd ${TCDIR}/bin
+	sed -i -e 's%chdir "./example/test";%chdir "../example/test";%' test.pl || die
+
+}
+
+src_compile() {
+	make all || die
+}
+
+src_install() {
+	cd ${TCDIR}/bin
+	dobin t_coffee \
+		blast_aln2fasta_aln.pl \
+		extract_from_pdb \
+		fasta_aln2fasta_aln_unique_name.pl \
+		fugue_client \
+		msf_aln2fasta_aln.pl \
+		t_coffee_dpa \
+		t_coffee_dpa2
+	insinto /usr/share/${PN}/lib
+	doins ${TCDIR}/html
+
+	dodoc ${TCDIR}/doc/README4T-COFFEE
+	insinto /usr/share/doc/${PF}
+	doins ${TCDIR}/doc/t_coffee{_doc.{doc,pdf},.pdf}
+
+	insinto /usr/share/${PN}/example/seq
+	doins ${TCDIR}/example/seq/*
+	insinto /usr/share/${PN}/example/test
+	doins ${TCDIR}/example/test/*.{aln,pep}
+}
+
+src_test() {
+	cd ${TCDIR}/bin
+	./test.pl || die
+}