academic/ViennaRNA: Added (C Library).
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Rob van Nues
Willy Sudiarto Raharjo
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# ViennaRNA Package
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A C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
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Amongst other things, our implementations allow you to:
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- predict minimum free energy secondary structures
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- calculate the partition function for the ensemble of structures
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- compute various equilibrium probabilities
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- calculate suboptimal structures in a given energy range
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- compute local structures in long sequences
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- predict consensus secondary structures from a multiple sequence alignment
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- predict melting curves
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- search for sequences folding into a given structure
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- compare two secondary structures
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- predict hybridization structures of two RNA molecules
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The package includes `Perl 5`, `Python 2`, and `Python 3` modules that give
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access to almost all functions of the C library from within the respective
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scripting languages.
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There is also a set of programs for analyzing sequence and distance
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data using split decomposition, statistical geometry, and cluster methods.
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They are not maintained any more and not built by default.
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The code very rarely uses static arrays, and all programs should work for
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sequences up to a length of 32,700 (if you have huge amounts of memory that
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is).
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#!/bin/sh
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# Slackware build script for ViennaRNA
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# Copyright 2018 Rob van Nues
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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PRGNAM=ViennaRNA
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VERSION=${VERSION:-2.4.11}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i486 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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fi
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CWD=$(pwd)
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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if [ "$ARCH" = "i486" ]; then
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SLKCFLAGS="-O2 -march=i486 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "i686" ]; then
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SLKCFLAGS="-O2 -march=i686 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "x86_64" ]; then
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SLKCFLAGS="-O2 -fPIC"
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LIBDIRSUFFIX="64"
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else
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SLKCFLAGS="-O2"
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LIBDIRSUFFIX=""
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fi
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set -e
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf $PRGNAM-$VERSION
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tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
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cd $PRGNAM-$VERSION
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chown -R root:root .
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find . \
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\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
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-exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
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-exec chmod 644 {} \;
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# You can configure some ViennaRNA features that are (not) compiled by default.
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# See the README.md for details. You can enable/disable a these features by
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# passing variables to the script (VAR=yes/no ./ViennaRNA.SlackBuild).
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# indicated parts can be included/omitted
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# not-included by default
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# - CLuster Analysis (AnalyseSeqs, AnalyseDists)
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# - Kinwalker (co-transcriptional folding)
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# included but can be omitted:
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# - Kinfold
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# - RNAforester
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# - RNAlocmin
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# - Swig (all scripting interfaces)
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# - Perl interface
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# - Python interface
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# - Python 3 interface
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# - Streaming SIMD Extension support
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# in the case of run time/ make/ or configure problems try turning off:
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# - Link Time Optimization (LTO)
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# for concurrent computation:
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# - OpenMP support (disabling makes RNAlib not entirely threadsafe)
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# - POSIX threads (pthread) support
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# in case the following cause problems with your own third-party program that links against RNAlib
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# for Z-score filtering via statically linked libsvm:
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# - SVM Z-score filter in RNALfold
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# - GNU Scientific Library for RNApvmin
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cluster="" ; [ "${CLUS:-no}" != "no" ] && cluster="--with-cluster"
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kinwalker="" ; [ "${KINW:-no}" != "no" ] && kinwalker="--with-kinwalker"
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forester="" ; [ "${FORE:-yes}" != "yes" ] && forester="--without-forester"
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kinfold="" ; [ "${KINF:-yes}" != "yes" ] && kinwalk="--without-kinfold"
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rnalocmin="" ; [ "${RLOC:-yes}" != "yes" ] && rnalocmin="--without-rnalocmin"
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perl="" ; [ "${PERL:-yes}" != "yes" ] && perl="--without-perl"
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python="" ; [ "${PYTH:-yes}" != "yes" ] && python="--without-python"
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python3="" ; [ "${PYT3:-yes}" != "yes" ] && python3="--without-python3"
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swig="" ; [ "${SWIG:-yes}" != "yes" ] && swig="--without-swig"
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simd="" ; [ "${SIMD:-yes}" != "yes" ] && simd="--disable-simd"
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lto="" ; [ "${LTO:-yes}" != "yes" ] && lto="--disable-lto"
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openmp="" ; [ "${OMP:-yes}" != "yes" ] && openmp="--disable-openmp"
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pthreads="" ; [ "${PTHR:-yes}" != "yes" ] && pthreads="--disable-pthreads"
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svm="" ; [ "${SVM:-yes}" != "yes" ] && svm="--without-svm"
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gsl="" ; [ "${GSL:-yes}" != "yes" ] && gsl="--without-gsl"
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CFLAGS="$SLKCFLAGS" \
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CXXFLAGS="$SLKCFLAGS" \
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./configure \
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--prefix=/usr \
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--libdir=/usr/lib$LIBDIRSUFFIX \
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--mandir=/usr/man \
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--docdir=/usr/doc/$PRGNAM-$VERSION \
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--build=$ARCH-slackware-linux \
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$cluster \
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$kinwalker \
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$forester \
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$kinfold \
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$rnalocmin \
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$perl \
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$python \
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$python3 \
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$swig \
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$simd \
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$lto \
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$openmp \
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$pthreads \
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$svm \
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$gsl || exit 1
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make
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make install DESTDIR=$PKG
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##from https://www.tbi.univie.ac.at/RNA/packages/arch/PKGBUILD
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cd misc
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make install DESTDIR=$PKG
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cd ..
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# cleanup after dirty install ...
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# install -dm755 $PKG/usr/bin/vendor_perl
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for perlscript in $PKG/usr/share/ViennaRNA/bin/*.pl ; do
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# mv "$perlscript" "$PKG/usr/bin/vendor_perl/"
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mv "$perlscript" "$PKG/usr/bin/"
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done
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# no need for that file it is outdated anyway
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rm $PKG/usr/share/info/dir
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#gzip info file
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gzip -9 $PKG/usr/share/info/*.info
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find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
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| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
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find $PKG/usr/man -type f -exec gzip -9 {} \;
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for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done
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find $PKG -name perllocal.pod \
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-o -name ".packlist" \
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-o -name "*.bs" \
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| xargs rm -f
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a \
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NEWS README.md AUTHORS COPYING THANKS INSTALL CHANGELOG.md license.txt \
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$PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
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@ -0,0 +1,10 @@
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PRGNAM="ViennaRNA"
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VERSION="2.4.11"
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HOMEPAGE="https://www.tbi.univie.ac.at/RNA"
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DOWNLOAD="https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.11.tar.gz"
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MD5SUM="114ea7450ef994404754abdc6cb45353"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES="grace gri"
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MAINTAINER="Rob van Nues"
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EMAIL="sborg63@disroot.org"
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@ -0,0 +1,19 @@
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# HOW TO EDIT THIS FILE:
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# The "handy ruler" below makes it easier to edit a package description.
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# Line up the first '|' above the ':' following the base package name, and
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# the '|' on the right side marks the last column you can put a character in.
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# You must make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':' except on otherwise blank lines.
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|-----handy-ruler------------------------------------------------------|
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ViennaRNA: VienaRNA (C Library)
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ViennaRNA:
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ViennaRNA: The ViennaRNA Package consists of a C code library and several
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ViennaRNA: stand-alone programs for the prediction and comparison of RNA
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ViennaRNA: secondary structures.
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ViennaRNA:
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ViennaRNA: Reference: Lorenz R, Bernhart SH, Höner Zu Siederdissen C, Tafe
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ViennaRNA: H, Flamm C, Stadler PF, Hofacker IL. ViennaRNA Package 2.0
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ViennaRNA: Algorithms Mol. Biol., 6:1 26, 2011, doi:10.1186/1748-7188-6-26
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ViennaRNA: Home: https://www.tbi.univie.ac.at/RNA
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ViennaRNA:
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