From: Olivier Fisette Date: Thu, 23 Dec 2004 16:08:38 +0000 (+0000) Subject: Moving to sci-biology/vienna-rna X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=d723c4903fc5558c7002e9866080b0cab242adb3;p=gentoo.git Moving to sci-biology/vienna-rna --- diff --git a/app-sci/vienna-rna/ChangeLog b/app-sci/vienna-rna/ChangeLog deleted file mode 100644 index 6762bf1a1356..000000000000 --- 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 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/app-sci/vienna-rna/Manifest b/app-sci/vienna-rna/Manifest deleted file mode 100644 index c3e9063c6a02..000000000000 --- a/app-sci/vienna-rna/Manifest +++ /dev/null @@ -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 deleted file mode 100644 index 7845c674494f..000000000000 --- a/app-sci/vienna-rna/files/digest-vienna-rna-1.4 +++ /dev/null @@ -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 index 7ad711ea797b..000000000000 --- a/app-sci/vienna-rna/metadata.xml +++ /dev/null @@ -1,26 +0,0 @@ - - - - - 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/app-sci/vienna-rna/vienna-rna-1.4.ebuild b/app-sci/vienna-rna/vienna-rna-1.4.ebuild deleted file mode 100644 index d588ecba5ec8..000000000000 --- 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 -}