slackbuilds/academic/RAxML/RAxML.SlackBuild

#!/bin/bash

# Slackware build script for RAxML

# Copyright 2019-2021 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.

cd $(dirname $0) ; CWD=$(pwd)

PRGNAM=RAxML
VERSION=${VERSION:-8.2.12}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
PKGTYPE=${PKGTYPE:-tgz}

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 $TMP
rm -rf standard-$PRGNAM-$VERSION
tar xvf $CWD/standard-$PRGNAM-$VERSION.tar.gz
cd standard-$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 {} \;

# Build executables with the default Slackware compiler flags.

# Sequential version
cp Makefile.gcc Makefile
sed -i "/^CFLAGS/s/=/+=/" Makefile
sed -i "s|raxmlHPC|raxml|g" Makefile
CFLAGS="$SLKCFLAGS" \
make -f Makefile -j1
install -D -m755 raxml $PKG/usr/bin/raxml

# Openmpi version
cp Makefile.MPI.gcc Makefile.MPI
sed -i "/^CFLAGS/s/=/+=/" Makefile.MPI
sed -i "s|raxmlHPC-MPI|raxml-MPI|g" Makefile.MPI
CFLAGS="$SLKCFLAGS" \
make -f Makefile.MPI -j1
install -D -m755 raxml-MPI $PKG/usr/bin/raxml-MPI

##########################################################################
### You are highly encouraged to try the other optimisations below for ###
### performance enhancements. Just uncomment the corresponding lines.  ###
##########################################################################

## Default sequential version
#make -f Makefile.gcc
#install -D -m755 raxmlHPC $PKG/usr/bin/raxmlHPC

#make -f Makefile.SSE3.gcc
#install -D -m755 raxmlHPC-SSE3 $PKG/usr/bin/raxmlHPC-SSE3

#make -f Makefile.AVX.gcc
#install -D -m755 raxmlHPC-AVX $PKG/usr/bin/raxmlHPC-AVX

## Pthreads version
#make -f Makefile.PTHREADS.gcc
#install -D -m755 raxmlHPC-PTHREADS $PKG/usr/bin/raxmlHPC-PTHREADS

#make -f Makefile.SSE3.PTHREADS.gcc
#install -D -m755 raxmlHPC-PTHREADS-SSE3 $PKG/usr/bin/raxmlHPC-PTHREADS-SSE3

#make -f Makefile.AVX.PTHREADS.gcc
#install -D -m755 raxmlHPC-PTHREADS-AVX $PKG/usr/bin/raxmlHPC-PTHREADS-AVX

## Default coarse-grain MPI version
#make -f Makefile.MPI.gcc
#install -D -m755 raxmlHPC-MPI $PKG/usr/bin/raxmlHPC-MPI

#make -f Makefile.SSE3.MPI.gcc
#install -D -m755 raxmlHPC-MPI-SSE3 $PKG/usr/bin/raxmlHPC-MPI-SSE3

#make -f Makefile.AVX.MPI.gcc
#install -D -m755 raxmlHPC-MPI-AVX $PKG/usr/bin/raxmlHPC-MPI-AVX

## Hybrid MPI/Pthreads version
#  Before using this version, please read this paper here:
#  http://sco.h-its.org/exelixis/pubs/Exelixis-RRDR-2010-3.pdf
#  and look at these slides:
#  http://sco.h-its.org/exelixis/resource/doc/Phylo100225.pdf
#make -f Makefile.HYBRID.gcc
#install -D -m755 raxmlHPC-HYBRID $PKG/usr/bin/raxmlHPC-HYBRID

#make -f Makefile.SSE3.HYBRID.gcc
#install -D -m755 raxmlHPC-HYBRID-SSE3 $PKG/usr/bin/raxmlHPC-HYBRID-SSE3

#make -f Makefile.AVX.HYBRID.gcc
#install -D -m755 raxmlHPC-HYBRID-AVX $PKG/usr/bin/raxmlHPC-HYBRID-AVX

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

# Copy the useful scripts
mkdir -p $PKG/usr/share/$PRGNAM
cp -a usefulScripts $PKG/usr/share/$PRGNAM

mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
cp -a README manual $PKG/usr/doc/$PRGNAM-$VERSION
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References

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