diff options
| -rw-r--r-- | academic/ViennaRNA/README | 28 | ||||
| -rw-r--r-- | academic/ViennaRNA/ViennaRNA.SlackBuild | 180 | ||||
| -rw-r--r-- | academic/ViennaRNA/ViennaRNA.info | 10 | ||||
| -rw-r--r-- | academic/ViennaRNA/slack-desc | 19 |
4 files changed, 237 insertions, 0 deletions
diff --git a/academic/ViennaRNA/README b/academic/ViennaRNA/README new file mode 100644 index 0000000000000..84581ebcf2fff --- /dev/null +++ b/academic/ViennaRNA/README @@ -0,0 +1,28 @@ +# ViennaRNA Package + +A C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. + +Amongst other things, our implementations allow you to: + +- predict minimum free energy secondary structures +- calculate the partition function for the ensemble of structures +- compute various equilibrium probabilities +- calculate suboptimal structures in a given energy range +- compute local structures in long sequences +- predict consensus secondary structures from a multiple sequence alignment +- predict melting curves +- search for sequences folding into a given structure +- compare two secondary structures +- predict hybridization structures of two RNA molecules + +The package includes `Perl 5`, `Python 2`, and `Python 3` modules that give +access to almost all functions of the C library from within the respective +scripting languages. + +There is also a set of programs for analyzing sequence and distance +data using split decomposition, statistical geometry, and cluster methods. +They are not maintained any more and not built by default. + +The code very rarely uses static arrays, and all programs should work for +sequences up to a length of 32,700 (if you have huge amounts of memory that +is). diff --git a/academic/ViennaRNA/ViennaRNA.SlackBuild b/academic/ViennaRNA/ViennaRNA.SlackBuild new file mode 100644 index 0000000000000..2165d6da28327 --- /dev/null +++ b/academic/ViennaRNA/ViennaRNA.SlackBuild @@ -0,0 +1,180 @@ +#!/bin/sh + +# Slackware build script for ViennaRNA + +# Copyright 2018 Rob van Nues +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +PRGNAM=ViennaRNA +VERSION=${VERSION:-2.4.11} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i486 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i486" ]; then + SLKCFLAGS="-O2 -march=i486 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find . \ + \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ + -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ + -exec chmod 644 {} \; + +# You can configure some ViennaRNA features that are (not) compiled by default. +# See the README.md for details. You can enable/disable a these features by +# passing variables to the script (VAR=yes/no ./ViennaRNA.SlackBuild). +# indicated parts can be included/omitted +# not-included by default +# - CLuster Analysis (AnalyseSeqs, AnalyseDists) +# - Kinwalker (co-transcriptional folding) +# included but can be omitted: +# - Kinfold +# - RNAforester +# - RNAlocmin +# - Swig (all scripting interfaces) +# - Perl interface +# - Python interface +# - Python 3 interface +# - Streaming SIMD Extension support +# in the case of run time/ make/ or configure problems try turning off: +# - Link Time Optimization (LTO) +# for concurrent computation: +# - OpenMP support (disabling makes RNAlib not entirely threadsafe) +# - POSIX threads (pthread) support +# in case the following cause problems with your own third-party program that links against RNAlib +# for Z-score filtering via statically linked libsvm: +# - SVM Z-score filter in RNALfold +# - GNU Scientific Library for RNApvmin + +cluster="" ; [ "${CLUS:-no}" != "no" ] && cluster="--with-cluster" +kinwalker="" ; [ "${KINW:-no}" != "no" ] && kinwalker="--with-kinwalker" +forester="" ; [ "${FORE:-yes}" != "yes" ] && forester="--without-forester" +kinfold="" ; [ "${KINF:-yes}" != "yes" ] && kinwalk="--without-kinfold" +rnalocmin="" ; [ "${RLOC:-yes}" != "yes" ] && rnalocmin="--without-rnalocmin" +perl="" ; [ "${PERL:-yes}" != "yes" ] && perl="--without-perl" +python="" ; [ "${PYTH:-yes}" != "yes" ] && python="--without-python" +python3="" ; [ "${PYT3:-yes}" != "yes" ] && python3="--without-python3" +swig="" ; [ "${SWIG:-yes}" != "yes" ] && swig="--without-swig" +simd="" ; [ "${SIMD:-yes}" != "yes" ] && simd="--disable-simd" +lto="" ; [ "${LTO:-yes}" != "yes" ] && lto="--disable-lto" +openmp="" ; [ "${OMP:-yes}" != "yes" ] && openmp="--disable-openmp" +pthreads="" ; [ "${PTHR:-yes}" != "yes" ] && pthreads="--disable-pthreads" +svm="" ; [ "${SVM:-yes}" != "yes" ] && svm="--without-svm" +gsl="" ; [ "${GSL:-yes}" != "yes" ] && gsl="--without-gsl" + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib$LIBDIRSUFFIX \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux \ + $cluster \ + $kinwalker \ + $forester \ + $kinfold \ + $rnalocmin \ + $perl \ + $python \ + $python3 \ + $swig \ + $simd \ + $lto \ + $openmp \ + $pthreads \ + $svm \ + $gsl || exit 1 + +make +make install DESTDIR=$PKG + +##from https://www.tbi.univie.ac.at/RNA/packages/arch/PKGBUILD +cd misc +make install DESTDIR=$PKG +cd .. + +# cleanup after dirty install ... +# install -dm755 $PKG/usr/bin/vendor_perl +for perlscript in $PKG/usr/share/ViennaRNA/bin/*.pl ; do +# mv "$perlscript" "$PKG/usr/bin/vendor_perl/" + mv "$perlscript" "$PKG/usr/bin/" +done + +# no need for that file it is outdated anyway +rm $PKG/usr/share/info/dir + +#gzip info file +gzip -9 $PKG/usr/share/info/*.info + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +find $PKG -name perllocal.pod \ + -o -name ".packlist" \ + -o -name "*.bs" \ + | xargs rm -f + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + NEWS README.md AUTHORS COPYING THANKS INSTALL CHANGELOG.md license.txt \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/ViennaRNA/ViennaRNA.info b/academic/ViennaRNA/ViennaRNA.info new file mode 100644 index 0000000000000..ffde773320486 --- /dev/null +++ b/academic/ViennaRNA/ViennaRNA.info @@ -0,0 +1,10 @@ +PRGNAM="ViennaRNA" +VERSION="2.4.11" +HOMEPAGE="https://www.tbi.univie.ac.at/RNA" +DOWNLOAD="https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.11.tar.gz" +MD5SUM="114ea7450ef994404754abdc6cb45353" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="grace gri" +MAINTAINER="Rob van Nues" +EMAIL="sborg63@disroot.org" diff --git a/academic/ViennaRNA/slack-desc b/academic/ViennaRNA/slack-desc new file mode 100644 index 0000000000000..e5d1921f61a71 --- /dev/null +++ b/academic/ViennaRNA/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +ViennaRNA: VienaRNA (C Library) +ViennaRNA: +ViennaRNA: The ViennaRNA Package consists of a C code library and several +ViennaRNA: stand-alone programs for the prediction and comparison of RNA +ViennaRNA: secondary structures. +ViennaRNA: +ViennaRNA: Reference: Lorenz R, Bernhart SH, Höner Zu Siederdissen C, Tafe +ViennaRNA: H, Flamm C, Stadler PF, Hofacker IL. ViennaRNA Package 2.0 +ViennaRNA: Algorithms Mol. Biol., 6:1 26, 2011, doi:10.1186/1748-7188-6-26 +ViennaRNA: Home: https://www.tbi.univie.ac.at/RNA +ViennaRNA: |