Moving to sci-biology/vienna-rna

diff --git a/app-sci/vienna-rna/ChangeLog b/app-sci/vienna-rna/ChangeLog
deleted file mode 100644 (file)
index 6762bf1..0000000
--- a/app-sci/vienna-rna/ChangeLog
+++ /dev/null
@@ -1,17 +0,0 @@
-# ChangeLog for app-sci/vienna-rna
-# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/vienna-rna/ChangeLog,v 1.4 2004/11/01 03:03:35 ribosome Exp $
-
-  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/app-sci/vienna-rna/Manifest b/app-sci/vienna-rna/Manifest
deleted file mode 100644 (file)
index c3e9063..0000000
--- a/app-sci/vienna-rna/Manifest
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@@ -1,4 +0,0 @@
-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/app-sci/vienna-rna/files/digest-vienna-rna-1.4 b/app-sci/vienna-rna/files/digest-vienna-rna-1.4
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index 7845c67..0000000
--- a/app-sci/vienna-rna/files/digest-vienna-rna-1.4
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@@ -1 +0,0 @@
-MD5 89df828c775783426e7d2db8b2fd42d4 ViennaRNA-1.4.tar.gz 483047

diff --git a/app-sci/vienna-rna/metadata.xml b/app-sci/vienna-rna/metadata.xml
deleted file mode 100644 (file)
index 7ad711e..0000000
--- a/app-sci/vienna-rna/metadata.xml
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@@ -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>
-               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/app-sci/vienna-rna/vienna-rna-1.4.ebuild b/app-sci/vienna-rna/vienna-rna-1.4.ebuild
deleted file mode 100644 (file)
index d588ecb..0000000
--- a/app-sci/vienna-rna/vienna-rna-1.4.ebuild
+++ /dev/null
@@ -1,76 +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/vienna-rna/vienna-rna-1.4.ebuild,v 1.4 2004/11/01 03:03:35 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
-}