slackbuilds/academic/samtools/samtools.SlackBuild

#!/bin/bash

# Slackware build script for samtools

# Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com
# Copyright 2017-2022 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=samtools
VERSION=${VERSION:-1.15.1}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
PKGTYPE=${PKGTYPE:-tgz}

# Some applications still rely on the legacy samtools API instead of using htslib 
# exclusively, in that case, install the headers in /usr/include/bam and the static 
# libbam library as well by declaring (uncommenting):
#SAMLIB="yes"
# and commenting out:
SAMLIB="no"

# WARNING: this package and htslib both provide a "sam.h" that aren't actually
# compatible with each other. Be extra careful about which file you're actually
# #including when using either of these packages for development work.


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.bz2
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 {} \;

# force linking to installed htslib
rm -r htslib-$VERSION

CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
  --prefix=/usr \
  --libdir=/usr/lib${LIBDIRSUFFIX} \
  --with-htslib=system \
  --mandir=/usr/man \
  --docdir=/usr/doc/$PRGNAM-$VERSION \
  --build=$ARCH-slackware-linux

make
make install DESTDIR=$PKG

mkdir -p $PKG/usr/share/$PRGNAM-$VERSION
cp -a misc/*.lua $PKG/usr/share/$PRGNAM-$VERSION

# include samtools-API if set above
if [ "$SAMLIB" = "yes" ] ; then
  mkdir -p $PKG/usr/include/bam
  mkdir -p $PKG/usr/lib${LIBDIRSUFFIX}
  install -m644 libbam.a "$PKG/usr/lib${LIBDIRSUFFIX}"
  install -m644 *.h "$PKG/usr/include/bam"
fi

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 LICENSE README INSTALL NEWS examples \
  $PKG/usr/doc/$PRGNAM-$VERSION
cp $CWD/README $PKG/usr/doc/$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