mirror of
https://github.com/Ponce/slackbuilds
synced 2024-11-24 10:02:29 +01:00
160 lines
5.6 KiB
Bash
160 lines
5.6 KiB
Bash
#!/bin/sh
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# Slackware build script for paml
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# Copyright 2013-2014 Petar Petrov, petar.petrov@student.oulu.fi
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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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PRGNAM=paml
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VERSION=${VERSION:-4.8a}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i486 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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fi
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MAINVER=4.8
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CWD=$(pwd)
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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if [ "$ARCH" = "i486" ]; then
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SLKCFLAGS="-O2 -march=i486 -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 ${PRGNAM}${VERSION}
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tar xvf $CWD/${PRGNAM}${VERSION}.tgz
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cd ${PRGNAM}${MAINVER}
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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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# Use our CFLAGS
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sed -i "/^C.*.*FLAGS/s/=/+=/" src/Makefile
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# These are the main components, and most likely this will be all you
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# need. Check the next sections if you need some optional components.
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# They will be installed to /usr/libexec/paml in case you want them.
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cd src
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CFLAGS="$SLKCFLAGS" \
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make -f Makefile
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install -D -m755 baseml $PKG/usr/bin/baseml
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install -D -m755 basemlg $PKG/usr/bin/basemlg
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install -D -m755 chi2 $PKG/usr/bin/chi2
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install -D -m755 codeml $PKG/usr/bin/codeml
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install -D -m755 evolver $PKG/usr/bin/evolver
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install -D -m755 mcmctree $PKG/usr/bin/mcmctree
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install -D -m755 pamp $PKG/usr/bin/pamp
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install -D -m755 yn00 $PKG/usr/bin/yn00
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# Compile and install Evolver variations
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cc $SLKCFLAGS -DCodonNSbranches -o evolverNSbranches evolver.c tools.c -lm
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cc $SLKCFLAGS -DCodonNSsites -o evolverNSsites evolver.c tools.c -lm
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cc $SLKCFLAGS -DCodonNSbranchsites -o evolverNSbranchsites evolver.c tools.c -lm
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install -D -m755 evolverNSbranches $PKG/usr/libexec/$PRGNAM/evolverNSbranches
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install -D -m755 evolverNSbranchsites $PKG/usr/libexec/$PRGNAM/evolverNSbranchsites
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install -D -m755 evolverNSsites $PKG/usr/libexec/$PRGNAM/evolverNSsites
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# Compile and install TreeTime
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cc $SLKCFLAGS -o TreeTimeJeff TreeTimeJeff.c tools.c -lm
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install -D -m755 TreeTimeJeff $PKG/usr/libexec/$PRGNAM/TreeTimeJeff
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# Rename the local README, so we include it in the package.
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mv README.txt README-compiling.txt
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# Compile and install NEB, BEB and BranchSite
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cd ../Technical/Simulation/Codon
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cc $SLKCFLAGS -DNEB -o PositiveSitesNEB PositiveSites.c -lm
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cc $SLKCFLAGS -DBEB -o PositiveSitesBEB PositiveSites.c -lm
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cc $SLKCFLAGS -DBranchSite -o PositiveSitesBS PositiveSites.c -lm
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install -D -m755 PositiveSitesBEB $PKG/usr/libexec/$PRGNAM/PositiveSitesBEB
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install -D -m755 PositiveSitesBS $PKG/usr/libexec/$PRGNAM/PositiveSitesBS
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install -D -m755 PositiveSitesNEB $PKG/usr/libexec/$PRGNAM/PositiveSitesNEB
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# Rename this README too so we include it in the package.
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mv README.txt README-codon.txt
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# Compile and install Multiruns
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cd ..
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cc -o multiruns $SLKCFLAGS multiruns.c -lm
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install -D -m755 multiruns $PKG/usr/libexec/$PRGNAM/multiruns
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cd $TMP/${PRGNAM}${MAINVER}
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# Include sample system files and example experimental data.
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mkdir -p $PKG/usr/share/$PRGNAM/{aa,codon,ctl,dat,nuc,paup,trees}
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cp -a *.dat dat/* $PKG/usr/share/$PRGNAM/dat
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cp -a Technical/Simulation/Codon/{codeml.ctl,*.dat} \
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$PKG/usr/share/$PRGNAM/codon
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cp -a examples $PKG/usr/share/$PRGNAM
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cp -a *.aa $PKG/usr/share/$PRGNAM/aa
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cp -a *.ctl $PKG/usr/share/$PRGNAM/ctl
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cp -a *.nuc $PKG/usr/share/$PRGNAM/nuc
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cp -a paup* $PKG/usr/share/$PRGNAM/paup
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cp -a *.trees $PKG/usr/share/$PRGNAM/trees
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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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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a README.txt GeneticCode.txt doc/* src/README-compiling.txt \
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Technical/{Pt/eigenQREV.pdf,Simulation/{multiruns.txt,Codon/README-codon.txt}}\
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$PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/MCMCtree.Tutorials.pdf > $PKG/usr/doc/$PRGNAM-$VERSION/MCMCtree.Tutorial.pdf
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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cat $CWD/LICENSE > $PKG/usr/doc/$PRGNAM-$VERSION/LICENSE
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# Fix permissions.
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find $PKG/usr/{doc,share} -type d -exec chmod 755 {} \; -o \
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-type f -exec chmod 644 {} \;
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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:-tgz}
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