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|
#!/bin/bash
# Slackware build script for PhyML
# Copyright 2011-2022 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.
# Thanks to Niels Horn for some handy modifications and corrections.
cd $(dirname $0) ; CWD=$(pwd)
PRGNAM=PhyML
VERSION=${VERSION:-3.3.20220408}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
PKGTYPE=${PKGTYPE:-tgz}
SRCNAM=$(echo $PRGNAM | tr A-Z a-z)
if [ -z "$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 $SRCNAM-$VERSION
tar xvf $CWD/$SRCNAM-$VERSION.tar.gz
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 {} \;
# This is PhyML, the main component of the package. If this is all you want, you
# can comment out the sections that build PhyML MPI and Phyrex below.
./autogen.sh
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--enable-phyml \
--docdir=/usr/doc/$PRGNAM-$VERSION \
--build=$ARCH-slackware-linux
# Use our CFLAGS
sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile
# The -mfma flag is needed for building on 14.2. Help is from here:
# https://github.com/horovod/horovod/issues/1832
CFLAGS="$SLKCFLAGS -mfma" CXXFLAGS="$SLKCFLAGS -mfma" make
make install DESTDIR=$PKG
# This is PhyML MPI. If you do not want it, comment the lines below. Then you do
# not need to install openmpi.
./autogen.sh
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--enable-mpi \
--docdir=/usr/doc/$PRGNAM-$VERSION \
--build=$ARCH-slackware-linux
# Use our CFLAGS
sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile
CFLAGS="$SLKCFLAGS -mfma" CXXFLAGS="$SLKCFLAGS -mfma" make
make install DESTDIR=$PKG
# This is Phyrex but it breaks at the moment
./autogen.sh
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--enable-phyrex \
--docdir=/usr/doc/$PRGNAM-$VERSION \
--build=$ARCH-slackware-linux
# Use our CFLAGS
sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile
CFLAGS="$SLKCFLAGS -mfma" CXXFLAGS="$SLKCFLAGS -mfma" make
make install DESTDIR=$PKG
# # This is PhyTime
# ./autogen.sh
# ./configure \
# --prefix=/usr \
# --libdir=/usr/lib${LIBDIRSUFFIX} \
# --sysconfdir=/etc \
# --localstatedir=/var \
# --mandir=/usr/man \
# --enable-phytime \
# --docdir=/usr/doc/$PRGNAM-$VERSION \
# --build=$ARCH-slackware-linux
#
# # Use our CFLAGS
# sed -i "/^CFLAGS/s/=/+=/" Makefile src/Makefile
#
# CFLAGS="$SLKCFLAGS -mfma" CXXFLAGS="$SLKCFLAGS -mfma" make
# make install DESTDIR=$PKG
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
# fix permissions for docs
chmod 0644 doc/*.{pdf,tex,bib}
chmod 0644 doc/fig/*.pdf
# Include some examples
mkdir -p $PKG/usr/share/$PRGNAM
cp -a examples $PKG/usr/share/$PRGNAM
mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
cp -a \
doc/{$SRCNAM-manual.pdf,ref.bib,$SRCNAM-manual.tex,fig} COPYING README.md \
$PKG/usr/doc/$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
|
