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# Maintainer: Malacology <guoyizhang at malacology dot net>
# Contributor: Malacology <guoyizhang at malacology dot net>
basename=beast
pkgname=('beast' 'beastgen' 'coalgen' 'phylogeography' 'pibuss')
pkgver=1.10.4
pkgrel=0
arch=('x86_64')
url="http://beast.community/"
license=('LGPL')
source=("https://github.com/beast-dev/beast-mcmc/archive/refs/tags/v${pkgver//__/-}.tar.gz"
"$basename.patch::https://patch-diff.githubusercontent.com/raw/beast-dev/beast-mcmc/pull/1149.patch")
sha256sums=('6e28e2df680364867e088acd181877a5d6a1d664f70abc6eccc2ce3a34f3c54a'
'2f65ebb8c45feed0b2969276c7caae147b83f4f1dd4fc5e1d705aada2c4163e1')
depends=('java-runtime=8')
makedepends=('java-environment=8' 'ant' 'cmake' 'beagle-lib' 'gendesk')
prepare(){
cd $srcdir/$basename-mcmc-${pkgver//__/-}
patch -p1 < $srcdir/$basename.patch
}
build() {
cd $srcdir/$basename-mcmc-${pkgver//__/-}
ant linux
java -jar -Djava.library.path=/usr/lib build/dist/beast.jar -beagle_info
cp -r build/dist dist_beast
ant -buildfile build_beastgen.xml package
cp -r dist dist_beastgen
ant -buildfile build_bss.xml linux
cp -r dist dist_pibuss
ant -buildfile build_coalsim.xml dist
cp -r dist dist_coalgen
ant -buildfile build_phylogeography.xml package
cp -r dist dist_phylogeography
ant -buildfile build_tempest.xml dist
cp -r dist dist_tempest
}
package_beast() {
pkgdesc="Bayesian Evolutionary Analysis Sampling Trees. https://doi.org/10.1186/1471-2148-7-214"
optdepends=('beagle-lib')
# install jar
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd dist_beast
for jar in $(ls *.jar)
do
install -Dm 755 $jar $pkgdir/usr/share/$pkgname/$jar
done
# install bin, desktop
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd release/Linux/scripts
sed -i "s@/usr/local/lib@/usr/lib@g" *
sed -i "s@\$BEAST/lib@/usr/share/beast@g" *
for bin in $(ls)
do
install -Dm 755 $bin $pkgdir/usr/bin/$pkgname-$bin
gendesk --pkgname "$bin" --pkgdesc "$pkgdesc" --exec="$pkgname-$bin" --icon="/usr/share/pixmaps/$bin.png"
install -Dm 755 $bin.desktop $pkgdir/usr/share/applications/$basename-$bin.desktop
done
# install icons
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd release/common/icons
for icon in $(ls *.png)
do
install -Dm 644 $icon $pkgdir/usr/share/pixmaps/${icon,,}
done
# ln icons
for png in loganalyser logcombiner treeannotator
do
ln -s /usr/share/pixmaps/utility.png $pkgdir/usr/share/pixmaps/$png.png
done
}
package_beastgen(){
pkgdesc="Bayesian Evolutionary Analysis Sampling Trees. https://doi.org/10.1186/1471-2148-7-214"
optdepends=('beagle-lib')
# install jar
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd dist_beastgen
install -Dm 755 $pkgname.jar $pkgdir/usr/share/$pkgname/$pkgname.jar
# install bin
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd release_beastgen/common/bin/
sed -i "s@\$BEASTGEN/lib@/usr/share/beastgen@g" beastgen
install -Dm 755 $pkgname $pkgdir/usr/bin/$pkgname
}
package_pibuss(){
pkgdesc="a BEAST/BEAGLE utility for sequence simulation, which provides an easy to use interface that allows flexible and extensible phylogenetic data fabrication. https://doi.org/10.1186/1471-2105-15-133"
optdepends=('beagle-lib')
# install jar
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd dist_pibuss
install -Dm 755 buss.jar $pkgdir/usr/share/$pkgname/buss.jar
# install bin
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd release_pibuss/Linux/scripts/
sed -i "s@/usr/local/lib@/usr/lib@g" pibuss
sed -i "s@\$PIBUSS/lib@/usr/share/pibuss@g" pibuss
install -Dm 755 $pkgname $pkgdir/usr/bin/$pkgname
# install icons
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd release_pibuss/Linux/icons
install -Dm 644 $pkgname.png $pkgdir/usr/share/pixmaps/$pkgname.png
# install pibuss.desktop
gendesk --pkgname "$pkgname" --pkgdesc "$pkgdesc" --exec="$pkgname" --icon="/usr/share/pixmaps/$pkgname.png"
install -Dm 755 $pkgname.desktop $pkgdir/usr/share/applications/$pkgname.desktop
}
package_coalgen(){
pkgdesc="BEAST Coalescent Tree Simulator https://doi.org/10.1186/1471-2148-7-214"
optdepends=('beagle-lib')
# install jar
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd dist_coalgen
install -Dm 755 $pkgname.jar $pkgdir/usr/share/$pkgname/$pkgname.jar
# install bin
echo "COALGEN_LIB=/usr/share/coalgen" >> $pkgname
echo "java -Xms64m -Xmx1024m -Djava.library.path=\"\$COALGEN_LIB:/usr/lib\" -jar \$COALGEN_LIB/coalgen.jar \$*" >> $pkgname
chmod +x $pkgname
install -Dm 755 $pkgname $pkgdir/usr/bin/$pkgname
# icon
cd $srcdir/$basename-mcmc-${pkgver//__/-}
install -Dm 644 src/dr/app/coalgen/images/CoalGen.png $pkgdir/usr/share/pixmaps/$pkgname.png
# desktop
gendesk --pkgname "$pkgname" --pkgdesc "$pkgdesc" --exec="$pkgname" --icon="/usr/share/pixmaps/$pkgname.png"
install -Dm 755 $pkgname.desktop $pkgdir/usr/share/applications/$pkgname.desktop
}
package_phylogeography(){
pkgdesc="BEAST PhyloGeography https://doi.org/10.1186/1471-2148-7-214"
optdepends=('beagle-lib')
# install jar
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd dist_$pkgname
install -Dm 755 $pkgname.jar $pkgdir/usr/share/$pkgname/$pkgname.jar
# install bin
cd $srcdir/$basename-mcmc-${pkgver//__/-}
cd release_phylogeography/common/bin/
for bin in continuous_tree_to_kml discrete_rate_prior_generator discrete_tree_to_kml rate_indicator_bf timeslicer
do
sed -i "s@\$PHYLOGEOGRAPHY/lib@/usr/share/phylogeography@g" $bin
install -Dm 755 $bin $pkgdir/usr/bin/$bin
done
}
#package_tempest(){
# pkgdesc="a tool for investigating the temporal signal and 'clocklikeness' of molecular phylogenies. https://doi.org/10.1093/ve/vew007"
#
# # install jar
# cd $srcdir/$basename-mcmc-${pkgver//__/-}
# cd dist_$pkgname
# install -Dm 755 $pkgname.jar $pkgdir/usr/share/$pkgname/$pkgname.jar
#
# # install bin
# echo "TEMPEST_LIB=/usr/share/tempest" >> $pkgname
# echo "java -Xms64m -Xmx1024m -Djava.library.path=\"\$TEMPEST_LIB:/usr/lib\" -jar \$TEMPEST_LIB/tempest.jar \$*" >> $pkgname
# chmod +x $pkgname
# install -Dm 755 $pkgname $pkgdir/usr/bin/$pkgname
#
# # install ico
# cd $srcdir/$basename-mcmc-${pkgver//__/-}
# cd release_$pkgname/Windows/icons
# install -Dm 644 TempEst.ico $pkgdir/usr/share/pixmaps/$pkgname.ico
#
# # desktop
# gendesk --pkgname "$pkgname" --pkgdesc "$pkgdesc" --exec="$pkgname" --icon="/usr/share/pixmaps/$pkgname.ico"
# install -Dm 755 $pkgname.desktop $pkgdir/usr/share/applications/$pkgname.desktop
#}
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