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

diff --git a/sci-biology/qrna/Manifest b/sci-biology/qrna/Manifest
index 204405420e3233fd780900b72b5f1467f32d0492..e6e86eab605e06d379221a6c434c391aa6035043 100644 (file)
--- a/sci-biology/qrna/Manifest
+++ b/sci-biology/qrna/Manifest
@@ -1,5 +1,5 @@
-MD5 b94191072e63a3e47c5ba416f3f72262 qrna-2.0.2c.ebuild 892
-MD5 bef5cd8ce639500ef42ff55452ea2bb9 ChangeLog 747
+MD5 6ccfb9d7cf660b0dc339d5ef8c9f85cc qrna-2.0.2c.ebuild 897
+MD5 87deff6fcb767760174d70664a7ac715 ChangeLog 933
 MD5 f189a3c4ff5ae55bcee4f8ed0ace5d20 metadata.xml 254
 MD5 9127b0a4628230fc3bf2e201ca7519a9 files/26qrna 30
 MD5 23a5277d2c657c4624bc93b197c51020 files/digest-qrna-2.0.2c 57

diff --git a/sci-biology/vienna-rna/ChangeLog b/sci-biology/vienna-rna/ChangeLog
new file mode 100644 (file)
index 0000000..7c993cc
--- /dev/null
+++ b/sci-biology/vienna-rna/ChangeLog
@@ -0,0 +1,23 @@
+# 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
new file mode 100644 (file)
index 0000000..c3e9063
--- /dev/null
+++ 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 (file)
index 0000000..7845c67
--- /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 (file)
index 0000000..7ad711e
--- /dev/null
+++ b/sci-biology/vienna-rna/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>
+               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 (file)
index 0000000..8c21f75
--- /dev/null
+++ b/sci-biology/vienna-rna/vienna-rna-1.4.ebuild
@@ -0,0 +1,76 @@
+# 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
+}