# Maintainer: Malacology # Contributor: Malacology 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 #}