Moved from app-sci/vienna-rna to sci-biology/vienna-rna.

5 files changed, 130 insertions, 0 deletions

diff --git a/sci-biology/vienna-rna/ChangeLog b/sci-biology/vienna-rna/ChangeLog
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+# ChangeLog for app-sci/vienna-rna
+# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.1 2004/12/23 16:09:31 ribosome Exp $
+
+*vienna-rna-1.4 (23 Dec 2004)
+
+  23 Dec 2004; Olivier Fisette <olivier@gentoo.org> +metadata.xml,
+  +vienna-rna-1.4.ebuild:
+  Moved from app-sci/vienna-rna to sci-biology/vienna-rna.
+
+  31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> vienna-rna-1.4.ebuild:
+  Added to x86.
+
+  23 Jun 2004; David Holm <dholm@gentoo.org> vienna-rna-1.4.ebuild:
+  Added to ~ppc.
+
+*vienna-rna-1.4 (22 Jun 2004)
+
+  22 Jun 2004; Olivier Fisette <ribosome@gentoo.org>
+  vienna-rna-1.4.ebuild, metadata.xml :
+  Initial import. Ebuild submitted by Olivier Fisette <ribosome@gentoo.org>.
+  Reference: Gentoo Bugzilla, bug #53734
+
diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest
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index 000000000000..c3e9063c6a02
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+++ b/sci-biology/vienna-rna/Manifest
@@ -0,0 +1,4 @@
+MD5 7de61d853da274edd7f6072d3939e813 vienna-rna-1.4.ebuild 2358
+MD5 c4cf62b17b2b077ac6b2b5a7a01366da ChangeLog 633
+MD5 07151097bf19cf3d886552b62d5f13c4 metadata.xml 1317
+MD5 f1a1d167e6d5e17687cee4ffb95c6044 files/digest-vienna-rna-1.4 65
diff --git a/sci-biology/vienna-rna/files/digest-vienna-rna-1.4 b/sci-biology/vienna-rna/files/digest-vienna-rna-1.4
new file mode 100644
index 000000000000..7845c674494f
--- /dev/null
+++ b/sci-biology/vienna-rna/files/digest-vienna-rna-1.4
@@ -0,0 +1 @@
+MD5 89df828c775783426e7d2db8b2fd42d4 ViennaRNA-1.4.tar.gz 483047
diff --git a/sci-biology/vienna-rna/metadata.xml b/sci-biology/vienna-rna/metadata.xml
new file mode 100644
index 000000000000..7ad711ea797b
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+++ b/sci-biology/vienna-rna/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>
+		The Vienna RNA Package consists of a C code library and several
+		stand-alone programs for the prediction and comparison of RNA secondary
+		structures. RNA secondary structure prediction through energy
+		minimization is the most used function in the package. We provide three
+		kinds of dynamic programming algorithms for structure prediction: the
+		minimum free energy algorithm of (Zuker and Stiegler 1981) which yields a
+		single optimal structure, the partition function algorithm of
+		(McCaskill 1990) which calculates base pair probabilities in the
+		thermodynamic ensemble, and the suboptimal folding algorithm of
+		(Wuchty et.al 1999) which generates all suboptimal structures within a
+		given energy range of the optimal energy. For secondary structure
+		comparison, the package contains several measures of distance
+		(dissimilarities) using either string alignment or tree-editing
+		(Shapiro and Zhang 1990). Finally, we provide an algorithm to design
+		sequences with a predefined structure (inverse folding).
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/vienna-rna/vienna-rna-1.4.ebuild b/sci-biology/vienna-rna/vienna-rna-1.4.ebuild
new file mode 100644
index 000000000000..8c21f75b2e12
--- /dev/null
+++ b/sci-biology/vienna-rna/vienna-rna-1.4.ebuild
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+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.4.ebuild,v 1.1 2004/12/23 16:09:31 ribosome Exp $
+
+inherit flag-o-matic
+
+DESCRIPTION="Vienna RNA Package - RNA secondary structure prediction and comparison"
+HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/"
+SRC_URI="http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-${PV}.tar.gz"
+LICENSE="vienna-rna"
+
+SLOT=0
+KEYWORDS="x86 ~ppc"
+IUSE="no-utils no-readseq perl"
+
+DEPEND="perl? ( dev-lang/perl )
+	!no-utils? ( dev-lang/perl )"
+
+S="${WORKDIR}/ViennaRNA-${PV}"
+
+src_compile() {
+	sed -ie 's:/usr/local/bin/perl:/usr/bin/perl:' Perl/RNAfold.pl
+	sed -ie 's:/usr/local/bin/perl:/usr/bin/perl:' Utils/ct2b.pl
+	sed -ie 's:/usr/local/bin/perl:/usr/bin/perl:' Utils/b2mt.pl
+	sed -ie 's:/usr/local/bin/perl:/usr/bin/perl:' Utils/dpzoom.pl
+	sed -ie 's:/usr/local/bin/perl:/usr/bin/perl:' Utils/mountain.pl
+	append-flags -I../H
+	make -e library programs gammel subopt || die
+	use perl && make -e perl || die
+	use no-utils || make -e util || die
+	use no-readseq || cd Readseq && make -e || die
+}
+
+src_install() {
+	insinto /usr/include/vienna-rna
+	doins H/*
+	dolib.a lib/libRNA.a
+	dobin Cluster/{AnalyseDists,AnalyseSeqs}
+	dobin Progs/RNA{distance,eval,fold,heat,inverse,pdist}
+	dobin Subopt/{RNAsubopt,popt}
+
+	dodoc CHANGES CREDITS README
+	doinfo man/RNAlib.info
+	newman man/AnalyseDists.man AnalyseDists.man.1
+	newman man/AnalyseSeqs.man AnalyseSeqs.man.1
+	newman man/RNAdistance.man RNAdistance.man.1
+	newman man/RNAeval.man RNAeval.man.1
+	newman man/RNAfold.man RNAfold.man.1
+	newman man/RNAheat.man RNAheat.man.1
+	newman man/RNAinverse.man RNAinverse.man.1
+	newman man/RNApdist.man RNApdist.man.1
+	newman Subopt/RNAsubopt.man RNAsubopt.man.1
+	dohtml man/RNAlib.html
+	insinto /usr/share/doc/${P}/pdf
+	doins man/RNAlib.pdf
+
+	if use perl; then
+		cd Perl
+		make install DESTDIR=${D} || die
+		dodoc RNA_wrap.doc
+		cd ${S}
+	fi
+
+	if ! use no-utils; then
+		dobin Utils/{b2ct,ct2b.pl,dpzoom.pl,mountain.pl,b2mt.pl,Fold,RNAplot}
+		newdoc Utils/README README.utils
+		newman Utils/RNAplot.man RNAplot.man.1
+	fi
+
+	if ! use no-readseq; then
+		newbin Readseq/readseq readseq-vienna
+		newdoc Readseq/Readme README.readseq
+		newdoc Readseq/Formats FORMATS.readseq
+		newdoc Readseq/README README.readseq-vienna
+	fi
+}