academic/ViennaRNA: Added (C Library).

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

4 files changed, 237 insertions, 0 deletions

diff --git a/academic/ViennaRNA/README b/academic/ViennaRNA/README
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+# 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
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index 0000000000..2165d6da28
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+++ b/academic/ViennaRNA/ViennaRNA.SlackBuild
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+#!/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
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+++ b/academic/ViennaRNA/ViennaRNA.info
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+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
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+++ b/academic/ViennaRNA/slack-desc
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+# 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: