#!/bin/sh # Slackware build script for bowtie2 # Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com # Copyright 2018 Rob van Nues sborg63@disroot.org # # 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=bowtie2 VERSION=${VERSION:-2.3.5.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi CWD=$(pwd) TMP=${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 -xvzf $CWD/$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 {} \; #Use our FLAGS #sed -i "/RELEASE_FLAGS/s/=/+=/" Makefile RELEASE_FLAGS+="$SLKCFLAGS" \ make install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM install -D -m755 $PRGNAM-align-l $PKG/usr/bin/$PRGNAM-align-l install -D -m755 $PRGNAM-build-l $PKG/usr/bin/$PRGNAM-build-l install -D -m755 $PRGNAM-align-s $PKG/usr/bin/$PRGNAM-align-s install -D -m755 $PRGNAM-build-s $PKG/usr/bin/$PRGNAM-build-s install -D -m755 $PRGNAM-build $PKG/usr/bin/$PRGNAM-build install -D -m755 $PRGNAM-inspect-l $PKG/usr/bin/$PRGNAM-inspect-l install -D -m755 $PRGNAM-inspect-s $PKG/usr/bin/$PRGNAM-inspect-s install -D -m755 $PRGNAM-inspect $PKG/usr/bin/$PRGNAM-inspect # Copy examples and scripts mkdir -p $PKG/usr/share/$PRGNAM cp -a \ example scripts \ $PKG/usr/share/$PRGNAM # Let's compress the reads and indexes gzip $PKG/usr/share/$PRGNAM/example/reads/*.fq gzip $PKG/usr/share/$PRGNAM/example/index/*.bt2 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 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ AUTHORS LICENSE MANUAL NEWS TUTORIAL VERSION doc \ $PKG/usr/doc/$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}