From dfe642932babc41ea76aa4a0386c01690c14fea5 Mon Sep 17 00:00:00 2001 From: Olivier Fisette Date: Thu, 23 Dec 2004 16:09:31 +0000 Subject: [PATCH] Moved from app-sci/vienna-rna to sci-biology/vienna-rna. --- sci-biology/qrna/Manifest | 4 +- sci-biology/vienna-rna/ChangeLog | 23 ++++++ sci-biology/vienna-rna/Manifest | 4 + .../vienna-rna/files/digest-vienna-rna-1.4 | 1 + sci-biology/vienna-rna/metadata.xml | 26 +++++++ sci-biology/vienna-rna/vienna-rna-1.4.ebuild | 76 +++++++++++++++++++ 6 files changed, 132 insertions(+), 2 deletions(-) create mode 100644 sci-biology/vienna-rna/ChangeLog create mode 100644 sci-biology/vienna-rna/Manifest create mode 100644 sci-biology/vienna-rna/files/digest-vienna-rna-1.4 create mode 100644 sci-biology/vienna-rna/metadata.xml create mode 100644 sci-biology/vienna-rna/vienna-rna-1.4.ebuild diff --git a/sci-biology/qrna/Manifest b/sci-biology/qrna/Manifest index 204405420e32..e6e86eab605e 100644 --- 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 index 000000000000..7c993ccbe3e5 --- /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 +metadata.xml, + +vienna-rna-1.4.ebuild: + Moved from app-sci/vienna-rna to sci-biology/vienna-rna. + + 31 Oct 2004; Olivier Fisette vienna-rna-1.4.ebuild: + Added to x86. + + 23 Jun 2004; David Holm vienna-rna-1.4.ebuild: + Added to ~ppc. + +*vienna-rna-1.4 (22 Jun 2004) + + 22 Jun 2004; Olivier Fisette + vienna-rna-1.4.ebuild, metadata.xml : + Initial import. Ebuild submitted by Olivier Fisette . + Reference: Gentoo Bugzilla, bug #53734 + diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest new file mode 100644 index 000000000000..c3e9063c6a02 --- /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 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 --- /dev/null +++ b/sci-biology/vienna-rna/metadata.xml @@ -0,0 +1,26 @@ + + + + + ribosome@gentoo.org + Olivier Fisette + + sci + + 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). + + 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 @@ -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 +} -- 2.26.2