#!/bin/bash # Slackware build script for samtools-legacy # Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com # 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. # With help about the install paths from Arch Linux AUR: # https://aur.archlinux.org/packages/sa/samtools/PKGBUILD PRGNAM=samtools-legacy VERSION=${VERSION:-0.1.19} BUILD=${BUILD:-2} TAG=${TAG:-_SBo} SRCNAM=samtools SUFFIX=legacy if [ -z "$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 $SRCNAM-$VERSION tar xvf $CWD/$SRCNAM-$VERSION.tar.bz2 cd $SRCNAM-$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 CFLAGS/CXXFLAGS sed -i "/^C.*.*FLAGS/s/=/+=/" Makefile CFLAGS="$SLKCFLAGS" \ make make razip # Install samtools, razip and bam library install -D -m755 samtools $PKG/usr/bin/samtools-$SUFFIX install -D -m755 razip $PKG/usr/bin/razip-$SUFFIX install -D -m644 libbam.a $PKG/usr/lib${LIBDIRSUFFIX}/libbam.a # Install bcftools its library and vsfutils cd bcftools install -D -m755 bcftools $PKG/usr/bin/bcftools-$SUFFIX install -D -m644 libbcf.a $PKG/usr/lib${LIBDIRSUFFIX}/libbcf.a install -D -m755 vcfutils.pl $PKG/usr/bin/vcfutils-$SUFFIX.pl # Include additional executables cd ../misc install -D -m755 ace2sam $PKG/usr/libexec/$PRGNAM/ace2sam install -D -m755 bamcheck $PKG/usr/libexec/$PRGNAM/bamcheck install -D -m755 maq2sam-long $PKG/usr/libexec/$PRGNAM/maq2sam-long install -D -m755 maq2sam-short $PKG/usr/libexec/$PRGNAM/maq2sam-short install -D -m755 md5fa $PKG/usr/libexec/$PRGNAM/md5fa install -D -m755 md5sum-lite $PKG/usr/libexec/$PRGNAM/md5sum-lite install -D -m755 wgsim $PKG/usr/libexec/$PRGNAM/wgsim # Include some scripts mkdir -p $PKG/usr/share/$PRGNAM cp -a \ *.pl *.lua *.py plot-bamcheck \ $PKG/usr/share/$PRGNAM # Include bam header files cd .. mkdir -p $PKG/usr/include/bam for f in *.h ; do install -m644 $f "$PKG/usr/include/bam" done # Install manpage install -D -m644 $SRCNAM.1 $PKG/usr/man/man1/$PRGNAM.1 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 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ AUTHORS COPYING INSTALL NEWS \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References # Fix permissions in the package... find $PKG/usr/{doc,include,share} \ -type d -exec chmod 755 {} \; -o \ -type f -exec chmod 644 {} \; 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}