mirror of
https://github.com/Ponce/slackbuilds
synced 2024-11-24 10:02:29 +01:00
158 lines
5.6 KiB
Bash
158 lines
5.6 KiB
Bash
#!/bin/sh
|
|
|
|
# Slackware build script for paml
|
|
|
|
# Copyright 2013-2018 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.
|
|
|
|
PRGNAM=paml
|
|
VERSION=${VERSION:-4.9h}
|
|
BUILD=${BUILD:-1}
|
|
TAG=${TAG:-_SBo}
|
|
|
|
if [ -z "$ARCH" ]; then
|
|
case "$( uname -m )" in
|
|
i?86) ARCH=i586 ;;
|
|
arm*) ARCH=arm ;;
|
|
*) ARCH=$( uname -m ) ;;
|
|
esac
|
|
fi
|
|
|
|
CWD=$(pwd)
|
|
TMP=${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 ${PRGNAM}${VERSION}
|
|
tar xvf $CWD/${PRGNAM}${VERSION}.tgz
|
|
cd ${PRGNAM}${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 {} \;
|
|
|
|
# Use our CFLAGS
|
|
sed -i "/^C.*.*FLAGS/s/=/+=/" src/Makefile
|
|
|
|
# These are the main components, and most likely this will be all you
|
|
# need. Check the next sections if you need some optional components.
|
|
# They will be installed to /usr/libexec/paml in case you want them.
|
|
cd src
|
|
CFLAGS="$SLKCFLAGS" \
|
|
make -f Makefile
|
|
|
|
install -D -m755 baseml $PKG/usr/bin/baseml
|
|
install -D -m755 basemlg $PKG/usr/bin/basemlg
|
|
install -D -m755 chi2 $PKG/usr/bin/chi2
|
|
install -D -m755 codeml $PKG/usr/bin/codeml
|
|
install -D -m755 evolver $PKG/usr/bin/evolver
|
|
install -D -m755 mcmctree $PKG/usr/bin/mcmctree
|
|
install -D -m755 pamp $PKG/usr/bin/pamp
|
|
install -D -m755 yn00 $PKG/usr/bin/yn00
|
|
|
|
# Compile and install Evolver variations
|
|
cc $SLKCFLAGS -DCodonNSbranches -o evolverNSbranches evolver.c tools.c -lm
|
|
cc $SLKCFLAGS -DCodonNSsites -o evolverNSsites evolver.c tools.c -lm
|
|
cc $SLKCFLAGS -DCodonNSbranchsites -o evolverNSbranchsites evolver.c tools.c -lm
|
|
|
|
install -D -m755 evolverNSbranches $PKG/usr/libexec/$PRGNAM/evolverNSbranches
|
|
install -D -m755 evolverNSbranchsites $PKG/usr/libexec/$PRGNAM/evolverNSbranchsites
|
|
install -D -m755 evolverNSsites $PKG/usr/libexec/$PRGNAM/evolverNSsites
|
|
|
|
# Compile and install TreeTime
|
|
cc $SLKCFLAGS -o TreeTimeJeff TreeTimeJeff.c tools.c -lm
|
|
install -D -m755 TreeTimeJeff $PKG/usr/libexec/$PRGNAM/TreeTimeJeff
|
|
|
|
# Rename the local README, so we include it in the package.
|
|
mv README.txt README-compiling.txt
|
|
|
|
# Compile and install NEB, BEB and BranchSite
|
|
cd ../Technical/Simulation/Codon
|
|
cc $SLKCFLAGS -DNEB -o PositiveSitesNEB PositiveSites.c -lm
|
|
cc $SLKCFLAGS -DBEB -o PositiveSitesBEB PositiveSites.c -lm
|
|
cc $SLKCFLAGS -DBranchSite -o PositiveSitesBS PositiveSites.c -lm
|
|
|
|
install -D -m755 PositiveSitesBEB $PKG/usr/libexec/$PRGNAM/PositiveSitesBEB
|
|
install -D -m755 PositiveSitesBS $PKG/usr/libexec/$PRGNAM/PositiveSitesBS
|
|
install -D -m755 PositiveSitesNEB $PKG/usr/libexec/$PRGNAM/PositiveSitesNEB
|
|
|
|
# Rename this README too so we include it in the package.
|
|
mv README.txt README-codon.txt
|
|
|
|
# Compile and install Multiruns
|
|
cd ..
|
|
cc -o multiruns $SLKCFLAGS multiruns.c -lm
|
|
install -D -m755 multiruns $PKG/usr/libexec/$PRGNAM/multiruns
|
|
|
|
cd $TMP/${PRGNAM}${VERSION}
|
|
|
|
# Include sample system files and example experimental data.
|
|
mkdir -p $PKG/usr/share/$PRGNAM/{aa,codon,ctl,dat,nuc,paup,trees}
|
|
cp -a *.dat dat/* $PKG/usr/share/$PRGNAM/dat
|
|
cp -a Technical/Simulation/Codon/{codeml.ctl,*.dat} \
|
|
$PKG/usr/share/$PRGNAM/codon
|
|
cp -a examples $PKG/usr/share/$PRGNAM
|
|
cp -a *.aa $PKG/usr/share/$PRGNAM/aa
|
|
cp -a *.ctl $PKG/usr/share/$PRGNAM/ctl
|
|
cp -a *.nuc $PKG/usr/share/$PRGNAM/nuc
|
|
cp -a paup* $PKG/usr/share/$PRGNAM/paup
|
|
cp -a *.trees $PKG/usr/share/$PRGNAM/trees
|
|
|
|
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
|
|
|
|
mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
|
|
cp -a README.txt GeneticCode.txt doc/* src/README-compiling.txt \
|
|
Technical/{Pt/eigenQREV.pdf,Simulation/{multiruns.txt,Codon/README-codon.txt}}\
|
|
$PKG/usr/doc/$PRGNAM-$VERSION
|
|
cat $CWD/MCMCtree.Tutorials.pdf > $PKG/usr/doc/$PRGNAM-$VERSION/MCMCtree.Tutorial.pdf
|
|
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
|
|
cat $CWD/LICENSE > $PKG/usr/doc/$PRGNAM-$VERSION/LICENSE
|
|
|
|
# Fix permissions.
|
|
find $PKG/usr/{doc,share} -type d -exec chmod 755 {} \; -o \
|
|
-type f -exec chmod 644 {} \;
|
|
|
|
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}
|