mirror of
https://github.com/Ponce/slackbuilds
synced 2024-11-22 19:44:21 +01:00
216 lines
6.9 KiB
Bash
216 lines
6.9 KiB
Bash
#!/bin/bash
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# Slackware build script for ViennaRNA
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# Copyright 2018-2023 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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cd $(dirname $0) ; CWD=$(pwd)
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PRGNAM=ViennaRNA
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VERSION=${VERSION:-2.6.4}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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PKGTYPE=${PKGTYPE:-tgz}
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# RNAxplorer requires lapacke (which requires lapack that requires blas)
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# but cannot see what blas is used for compiling lapack
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# please adjust $BLAS to the blas installed on your system
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BLAS=${BLAS:-openblas}
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i586 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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fi
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if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then
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echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE"
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exit 0
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fi
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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 [ "$ARCH" = "i586" ]; then
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SLKCFLAGS="-O2 -march=i586 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$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 -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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-o -perm 511 \) -exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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# https://github.com/ViennaRNA/ViennaRNA/issues/243
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patch -p1 < $CWD/swig_4.2.0.txt
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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 3 interface (= Python 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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# everything is enabled here
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cluster="" ; [ "${CLUSTER:-yes}" != "no" ] && cluster="--with-cluster"
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kinwalker="" ; [ "${KINWALKER:-yes}" != "no" ] && kinwalker="--with-kinwalker"
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# Default enabled features:
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forester="" ; [ "${FORESTER:-yes}" != "no" ] && forester="--with-forester"
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kinfold="" ; [ "${KINFOLD:-yes}" != "no" ] && kinfold="--with-kinfold"
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rnalocmin="" ; [ "${RNALOCMIN:-yes}" != "no" ] && rnalocmin="--with-rnalocmin"
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perl="" ; [ "${PERL:-yes}" != "no" ] && perl="--with-perl"
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# python = python3
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python="" ; [ "${PYTHON:-yes}" != "no" ] && python="--with-python"
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swig="" ; [ "${SWIG:-yes}" != "no" ] && swig="--with-swig"
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simd="" ; [ "${SIMD:-yes}" != "no" ] && simd="--enable-simd"
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lto="" ; [ "${LTO:-yes}" != "no" ] && lto="--enable-lto"
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openmp="" ; [ "${OPENMP:-yes}" != "no" ] && openmp="--enable-openmp"
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pthreads="" ; [ "${PTHREADS:-yes}" != "no" ] && pthreads="--enable-pthreads"
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svm="" ; [ "${SVM:-yes}" != "no" ] && svm="--with-svm"
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gsl="" ; [ "${GSL:-yes}" != "no" ] && gsl="--with-gsl"
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json="" ; [ "${JSON:-yes}" != "no" ] && json="--with-json"
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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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--with-blas=$BLAS \
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--with-python2=no \
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--with-doc=no \
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$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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$swig \
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$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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$gsl \
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$json \
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|| 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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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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# cleanup after dirty install ...
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for perlscript in $PKG/usr/share/ViennaRNA/bin/*.pl ; do
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mv "$perlscript" "$PKG/usr/bin/"
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done
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rm -r $PKG/usr/share/ViennaRNA/bin
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# re-organise info files the Slackware/SBo way
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mkdir $PKG/usr/info/
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rm $PKG/usr/share/info/dir
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#gzip and move info file
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gzip -9 $PKG/usr/share/info/*.info*
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mv $PKG/usr/share/info/*.info* $PKG/usr/info/
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rmdir $PKG/usr/share/info
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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-$VERSION
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#keep help and RNAlib-${VERSION} in src
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if [[ -d $PKG/usr/doc/$PRGNAM-$VERSION/html ]]; then
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rm -r $PKG/usr/doc/$PRGNAM-$VERSION/html
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fi
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if [[ -e $PKG/usr/doc/$PRGNAM-$VERSION/RNAlib-$VERSION.pdf ]]; then
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rm $PKG/usr/doc/$PRGNAM-$VERSION/RNAlib-$VERSION.pdf
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fi
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cp -a \
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NEWS README.md AUTHORS COPYING THANKS 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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rm -f $PKG/usr/lib*/*.la
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cat $CWD/doinst.sh > $PKG/install/doinst.sh
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cat $CWD/douninst.sh > $PKG/install/douninst.sh
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE
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