mirror of
https://github.com/Ponce/slackbuilds
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113 lines
3.5 KiB
Bash
113 lines
3.5 KiB
Bash
#!/bin/sh
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# Slackware build script for bowtie2
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# Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com
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# Copyright 2018 Rob van Nues sborg63@disroot.org
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#
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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=bowtie2
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VERSION=${VERSION:-2.3.4.3}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i586 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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fi
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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" = "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 -xvzf $CWD/$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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#Use our FLAGS
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#sed -i "/RELEASE_FLAGS/s/=/+=/" Makefile
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RELEASE_FLAGS+="$SLKCFLAGS" \
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make
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install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM
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install -D -m755 $PRGNAM-align-l $PKG/usr/bin/$PRGNAM-align-l
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install -D -m755 $PRGNAM-build-l $PKG/usr/bin/$PRGNAM-build-l
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install -D -m755 $PRGNAM-align-s $PKG/usr/bin/$PRGNAM-align-s
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install -D -m755 $PRGNAM-build-s $PKG/usr/bin/$PRGNAM-build-s
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install -D -m755 $PRGNAM-build $PKG/usr/bin/$PRGNAM-build
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install -D -m755 $PRGNAM-inspect-l $PKG/usr/bin/$PRGNAM-inspect-l
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install -D -m755 $PRGNAM-inspect-s $PKG/usr/bin/$PRGNAM-inspect-s
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install -D -m755 $PRGNAM-inspect $PKG/usr/bin/$PRGNAM-inspect
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# Copy examples and scripts
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mkdir -p $PKG/usr/share/$PRGNAM
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cp -a \
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example scripts \
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$PKG/usr/share/$PRGNAM
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# Let's compress the reads and indexes
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gzip $PKG/usr/share/$PRGNAM/example/reads/*.fq
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gzip $PKG/usr/share/$PRGNAM/example/index/*.bt2
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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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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a \
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AUTHORS LICENSE MANUAL NEWS TUTORIAL VERSION doc \
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$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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