mirror of
https://github.com/Ponce/slackbuilds
synced 2024-11-22 19:44:21 +01:00
165 lines
5.3 KiB
Bash
165 lines
5.3 KiB
Bash
#!/bin/bash
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# Slackware build script for RAxML
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# Copyright 2019-2021 Petar Petrov slackalaxy@gmail.com
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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cd $(dirname $0) ; CWD=$(pwd)
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PRGNAM=RAxML
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VERSION=${VERSION:-8.2.12}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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PKGTYPE=${PKGTYPE:-tgz}
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i586 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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fi
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# If the variable PRINT_PACKAGE_NAME is set, then this script will report what
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# the name of the created package would be, and then exit. This information
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# could be useful to other scripts.
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if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then
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echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE"
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exit 0
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fi
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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if [ "$ARCH" = "i586" ]; then
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SLKCFLAGS="-O2 -march=i586 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "i686" ]; then
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SLKCFLAGS="-O2 -march=i686 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "x86_64" ]; then
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SLKCFLAGS="-O2 -fPIC"
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LIBDIRSUFFIX="64"
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else
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SLKCFLAGS="-O2"
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LIBDIRSUFFIX=""
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fi
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set -e
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf standard-$PRGNAM-$VERSION
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tar xvf $CWD/standard-$PRGNAM-$VERSION.tar.gz
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cd standard-$PRGNAM-$VERSION
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chown -R root:root .
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find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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-o -perm 511 \) -exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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# Build executables with the default Slackware compiler flags.
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# Sequential version
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cp Makefile.gcc Makefile
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sed -i "/^CFLAGS/s/=/+=/" Makefile
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sed -i "s|raxmlHPC|raxml|g" Makefile
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CFLAGS="$SLKCFLAGS" \
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make -f Makefile -j1
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install -D -m755 raxml $PKG/usr/bin/raxml
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# Openmpi version
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cp Makefile.MPI.gcc Makefile.MPI
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sed -i "/^CFLAGS/s/=/+=/" Makefile.MPI
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sed -i "s|raxmlHPC-MPI|raxml-MPI|g" Makefile.MPI
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CFLAGS="$SLKCFLAGS" \
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make -f Makefile.MPI -j1
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install -D -m755 raxml-MPI $PKG/usr/bin/raxml-MPI
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##########################################################################
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### You are highly encouraged to try the other optimisations below for ###
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### performance enhancements. Just uncomment the corresponding lines. ###
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##########################################################################
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## Default sequential version
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#make -f Makefile.gcc
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#install -D -m755 raxmlHPC $PKG/usr/bin/raxmlHPC
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#make -f Makefile.SSE3.gcc
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#install -D -m755 raxmlHPC-SSE3 $PKG/usr/bin/raxmlHPC-SSE3
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#make -f Makefile.AVX.gcc
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#install -D -m755 raxmlHPC-AVX $PKG/usr/bin/raxmlHPC-AVX
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## Pthreads version
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#make -f Makefile.PTHREADS.gcc
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#install -D -m755 raxmlHPC-PTHREADS $PKG/usr/bin/raxmlHPC-PTHREADS
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#make -f Makefile.SSE3.PTHREADS.gcc
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#install -D -m755 raxmlHPC-PTHREADS-SSE3 $PKG/usr/bin/raxmlHPC-PTHREADS-SSE3
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#make -f Makefile.AVX.PTHREADS.gcc
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#install -D -m755 raxmlHPC-PTHREADS-AVX $PKG/usr/bin/raxmlHPC-PTHREADS-AVX
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## Default coarse-grain MPI version
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#make -f Makefile.MPI.gcc
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#install -D -m755 raxmlHPC-MPI $PKG/usr/bin/raxmlHPC-MPI
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#make -f Makefile.SSE3.MPI.gcc
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#install -D -m755 raxmlHPC-MPI-SSE3 $PKG/usr/bin/raxmlHPC-MPI-SSE3
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#make -f Makefile.AVX.MPI.gcc
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#install -D -m755 raxmlHPC-MPI-AVX $PKG/usr/bin/raxmlHPC-MPI-AVX
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## Hybrid MPI/Pthreads version
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# Before using this version, please read this paper here:
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# http://sco.h-its.org/exelixis/pubs/Exelixis-RRDR-2010-3.pdf
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# and look at these slides:
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# http://sco.h-its.org/exelixis/resource/doc/Phylo100225.pdf
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#make -f Makefile.HYBRID.gcc
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#install -D -m755 raxmlHPC-HYBRID $PKG/usr/bin/raxmlHPC-HYBRID
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#make -f Makefile.SSE3.HYBRID.gcc
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#install -D -m755 raxmlHPC-HYBRID-SSE3 $PKG/usr/bin/raxmlHPC-HYBRID-SSE3
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#make -f Makefile.AVX.HYBRID.gcc
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#install -D -m755 raxmlHPC-HYBRID-AVX $PKG/usr/bin/raxmlHPC-HYBRID-AVX
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find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
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| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
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# Copy the useful scripts
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mkdir -p $PKG/usr/share/$PRGNAM
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cp -a usefulScripts $PKG/usr/share/$PRGNAM
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a README manual $PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE
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