#!/bin/bash
# Slackware build script for ViennaRNA
# Copyright 2018-2021 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.
cd $(dirname $0) ; CWD=$(pwd)
PRGNAM=ViennaRNA
VERSION=${VERSION:-2.5.0}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
PKGTYPE=${PKGTYPE:-tgz}
if [ -z "$ARCH" ]; then
case "$( uname -m )" in
i?86) ARCH=i586 ;;
arm*) ARCH=arm ;;
*) ARCH=$( uname -m ) ;;
esac
fi
# If the variable PRINT_PACKAGE_NAME is set, then this script will report what
# the name of the created package would be, and then exit. This information
# could be useful to other scripts.
if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then
echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE"
exit 0
fi
TMP=${TMP:-/tmp/SBo}
PKG=$TMP/package-$PRGNAM
OUTPUT=${OUTPUT:-/tmp}
if [ "$ARCH" = "i586" ]; then
SLKCFLAGS="-O2 -march=i586 -mtune=i686"
LIBDIRSUFFIX=""
elif [ "$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 -L . \
\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
-o -perm 511 \) -exec chmod 755 {} \; -o \
\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
-o -perm 440 -o -perm 400 \) -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="" ; [ "${CLUSTER:-yes}" != "no" ] && cluster="--with-cluster"
kinwalker="" ; [ "${KINWALKER:-yes}" != "no" ] && kinwalker="--with-kinwalker"
# Default enabled features:
forester="" ; [ "${FORESTER:-yes}" != "no" ] && forester="--with-forester"
kinfold="" ; [ "${KINFOLD:-yes}" != "no" ] && kinwalk="--with-kinfold"
rnalocmin="" ; [ "${RNALOCMIN:-yes}" != "no" ] && rnalocmin="--with-rnalocmin"
perl="" ; [ "${PERL:-yes}" != "no" ] && perl="--with-perl"
# python = python3
python="" ; [ "${PYTHON:-yes}" != "no" ] && python="--with-python"
swig="" ; [ "${SWIG:-yes}" != "no" ] && swig="--with-swig"
simd="" ; [ "${SIMD:-yes}" != "no" ] && simd="--enable-simd"
lto="" ; [ "${LTO:-yes}" != "no" ] && lto="--enable-lto"
openmp="" ; [ "${OPENMP:-yes}" != "no" ] && openmp="--enable-openmp"
pthreads="" ; [ "${PTHREADS:-yes}" != "no" ] && pthreads="--enable-pthreads"
svm="" ; [ "${SVM:-yes}" != "no" ] && svm="--with-svm"
gsl="" ; [ "${GSL:-yes}" != "no" ] && gsl="--with-gsl"
json="" ; [ "${JSON:-yes}" != "no" ] && json="--with-json"
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib$LIBDIRSUFFIX \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION \
--build=$ARCH-slackware-linux \
--with-python2=no \
--with-doc=no \
$cluster \
$kinwalker \
$forester \
$cluster \
$kinwalker \
$forester \
$kinfold \
$rnalocmin \
$perl \
$python \
$swig \
$simd \
$lto \
$openmp \
$pthreads \
$svm \
$gsl \
$json \
|| exit 1
make
make install DESTDIR=$PKG
##from https://www.tbi.univie.ac.at/RNA/packages/arch/PKGBUILD
cd misc
make install DESTDIR=$PKG
cd ..
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
# cleanup after dirty install ...
for perlscript in $PKG/usr/share/ViennaRNA/bin/*.pl ; do
mv "$perlscript" "$PKG/usr/bin/"
done
rm -r $PKG/usr/share/ViennaRNA/bin
# 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/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-$VERSION
#keep help and RNAlib-${VERSION} in src
if [[ -d $PKG/usr/doc/$PRGNAM-$VERSION/html ]]; then
rm -r $PKG/usr/doc/$PRGNAM-$VERSION/html
fi
if [[ -e $PKG/usr/doc/$PRGNAM-$VERSION/RNAlib-$VERSION.pdf ]]; then
rm $PKG/usr/doc/$PRGNAM-$VERSION/RNAlib-$VERSION.pdf
fi
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
|
