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# Maintainer: Malacology <guoyizhang at malacology dot com>
# Contributor: Malacology <guoyizhang at malacology dot com>
pkgname=beast2
pkgver=2.6.3
pkgrel=1
pkgdesc="Bayesian Evolutionary Analysis by Sampling Trees"
arch=('x86_64')
url="http://www.beast2.org/"
license=('LGPL-2.1 License')
source=("https://github.com/CompEvol/beast2/releases/download/v${pkgver}/BEAST.v${pkgver}.Linux.tgz")
sha256sums=('8899277b0d7124ab04dc512444d45f0f1a13505f3ce641e1f117098be3e2e20d')
depends=(
'jre-openjdk-headless'
'jre-openjdk'
'jdk-openjdk'
'openjdk-doc'
'openjdk-src'
)
package() {
mkdir "${pkgdir}/usr"
mkdir "${pkgdir}/usr/bin"
mkdir "${pkgdir}/usr/share"
mkdir "${pkgdir}/usr/share/applications"
mkdir "${pkgdir}/usr/share/beast2"
mkdir "${pkgdir}/usr/share/beast2/bin"
mkdir "${pkgdir}/usr/share/beast2/images"
mkdir "${pkgdir}/usr/share/beast2/lib"
install -m 755 ${srcdir}/beast/bin/applauncher ${pkgdir}/usr/share/beast2/bin/applauncher
install -m 755 ${srcdir}/beast/bin/beast ${pkgdir}/usr/share/beast2/bin/beast
install -m 755 ${srcdir}/beast/bin/beauti ${pkgdir}/usr/share/beast2/bin/beauti
install -m 755 ${srcdir}/beast/bin/densitree ${pkgdir}/usr/share/beast2/bin/densitree
install -m 755 ${srcdir}/beast/bin/loganalyser ${pkgdir}/usr/share/beast2/bin/loganalyser
install -m 755 ${srcdir}/beast/bin/logcombiner ${pkgdir}/usr/share/beast2/bin/logcombiner
install -m 755 ${srcdir}/beast/bin/packagemanager ${pkgdir}/usr/share/beast2/bin/packagemanager
install -m 755 ${srcdir}/beast/bin/treeannotator ${pkgdir}/usr/share/beast2/bin/treeannotator
install -m 755 ${srcdir}/beast/lib/beast.jar ${pkgdir}/usr/share/beast2/lib/beast.jar
install -m 755 ${srcdir}/beast/lib/beast.src.jar ${pkgdir}/usr/share/beast2/lib/beast.src.jar
install -m 755 ${srcdir}/beast/lib/DensiTree.jar ${pkgdir}/usr/share/beast2/lib/DensiTree.jar
install -m 755 ${srcdir}/beast/lib/launcher.jar ${pkgdir}/usr/share/beast2/lib/launcher.jar
install -m 755 ${srcdir}/beast/images/beast.png ${pkgdir}/usr/share/beast2/images/beast.png
install -m 755 ${srcdir}/beast/images/beauti.png ${pkgdir}/usr/share/beast2/images/beauti.png
install -m 755 ${srcdir}/beast/images/DensiTree.png ${pkgdir}/usr/share/beast2/images/DensiTree.png
install -m 755 ${srcdir}/beast/LICENSE.txt ${pkgdir}/usr/share/beast2/LICENSE.txt
install -m 755 ${srcdir}/beast/README.txt ${pkgdir}/usr/share/beast2/README.txt
install -m 755 "${srcdir}/beast/VERSION HISTORY.txt" "${pkgdir}/usr/share/beast2/VERSION HISTORY.txt"
ln -s /usr/share/beast2/bin/beauti ${pkgdir}/usr/bin/beauti
ln -s /usr/share/beast2/bin/logcombiner ${pkgdir}/usr/bin/logcombiner
ln -s /usr/share/beast2/bin/treeannotator ${pkgdir}/usr/bin/treeannotator
ln -s /usr/share/beast2/bin/densitree ${pkgdir}/usr/bin/densitree
cp ~/.cache/yay/beast2/beauti.desktop ${pkgdir}/usr/share/applications
cp ~/.cache/yay/beast2/densitree.desktop ${pkgdir}/usr/share/applications
cp ~/.cache/yay/beast2/logcombiner.desktop ${pkgdir}/usr/share/applications
cp ~/.cache/yay/beast2/treeannotator.desktop ${pkgdir}/usr/share/applications
}
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