slackbuilds/academic/mafft/mafft.SlackBuild

#!/bin/sh

# Slackware build script for mafft

# Copyright 2013-2015 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.

PRGNAM=mafft
VERSION=${VERSION:-7.221}
BUILD=${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-with-extensions
tar xvf $CWD/$PRGNAM-$VERSION-with-extensions-src.tgz
cd $PRGNAM-$VERSION-with-extensions
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 {} \;

cd core
make clean
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
PREFIX=/usr \
LIBDIR=/usr/libexec/$PRGNAM \
MANDIR=/usr/man/man1 \
make -e

cd ../extensions
make clean
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
PREFIX=/usr \
LIBDIR=/usr/libexec/$PRGNAM \
MANDIR=/usr/man/man1 \
make -e

cd ../core
make \
PREFIX=$PKG/usr \
LIBDIR=$PKG/usr/libexec/$PRGNAM \
MANDIR=$PKG/usr/man/man1 \
install

cd ../extensions
make \
PREFIX=$PKG/usr \
LIBDIR=$PKG/usr/libexec/$PRGNAM \
MANDIR=$PKG/usr/man/man1 \
install

cd ..

# Clean up
rm -rf $PKG/usr/libexec/$PRGNAM/{$PRGNAM.1,$PRGNAM-homologs.1}

# Fix two wrong links
( cd $PKG/usr/bin
  rm -f mafft-distance mafft-profile
  ln -s /usr/libexec/mafft/mafft-distance mafft-distance
  ln -s /usr/libexec/mafft/mafft-profile mafft-profile )

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 \
  license license.extensions readme \
  $PKG/usr/doc/$PRGNAM-$VERSION
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References

# Fix permissions
find $PKG/usr/doc -type f -exec chmod 0644 {} \;

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}