slackbuilds/academic/samtools/samtools.SlackBuild

#!/bin/sh

# Slackware build script for samtools

# Copyright 2013 Petar Petrov, petar.petrov@student.oulu.fi
# 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	
VERSION=${VERSION:-0.1.19}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}

if [ -z "$ARCH" ]; then
  case "$( uname -m )" in
    i?86) ARCH=i486 ;;
    arm*) ARCH=arm ;;
       *) ARCH=$( uname -m ) ;;
  esac
fi

CWD=$(pwd)
TMP=${TMP:-/tmp/SBo}
PKG=$TMP/package-$PRGNAM
OUTPUT=${OUTPUT:-/tmp}

if [ "$ARCH" = "i486" ]; then
  SLKCFLAGS="-O2 -march=i486 -mtune=i686"
  LIBDIRSUFFIX=""
elif [ "$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 {} \;

# 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
install -D -m755 razip	  $PKG/usr/bin/razip
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
install -D -m644 libbcf.a $PKG/usr/lib${LIBDIRSUFFIX}/libbcf.a
install -D -m755 vcfutils.pl $PKG/usr/bin/vcfutils.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 $PRGNAM.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}