beast2: build from source

BioArchLinux/beast2/PKGBUILD

@@ -2,15 +2,19 @@
 # Contributor: Malacology <guoyizhang at malacology dot com>
 
 pkgname=beast2
-pkgver=2.7.1
+pkgver=2.7.2
 pkgrel=1
 pkgdesc="Bayesian Evolutionary Analysis by Sampling Trees. https://doi.org/10.1371/journal.pcbi.1003537"
 arch=('x86_64')
 url="http://www.beast2.org/"
 license=('LGPL')
-provides=("beast2")
-source=("https://github.com/CompEvol/beast2/releases/download/v${pkgver}/BEAST.v${pkgver}.Linux.x86.tgz" "beauti.desktop" "densitree.desktop" "logcombiner.desktop" "treeannotator.desktop" "beast2.desktop" "loganalyser.desktop" "applauncher.desktop")
-sha256sums=('959ff0336a0e87637e0381aa88b22c4e9f5929319fcc69e4c5bdfadb18b97eb3'
+source=("${pkgname}-${pkgver}.tar.gz::https://github.com/CompEvol/beast2/archive/refs/tags/${pkgver}.tar.gz"
+"git+https://github.com/CompEvol/BeastFX.git#commit=e6c9fdb2"
+ "beauti.desktop" "densitree.desktop" "logcombiner.desktop" "treeannotator.desktop" "beast2.desktop"
+ "loganalyser.desktop" "applauncher.desktop"
+)
+sha256sums=('02f561f593adf54e512d34a9366dd9e4ed0b940cb4540d97a2b4e9b705f327a3'
+            'SKIP'
             '83fba4c776fd29d6852c9c412c31d98bff657e2d2d2763dfe46d4c6174a9495f'
             '40d86086691b6cb91d0af54e5dc53d6693e084242ff3cc77862650ca78667c3d'
             'c2057c6ac656e13dcfbdf580a696bc79cb22c3d5270d546eac3e2fb42d620f20'
@@ -18,16 +22,31 @@ sha256sums=('959ff0336a0e87637e0381aa88b22c4e9f5929319fcc69e4c5bdfadb18b97eb3'
             'cf09789425aec65601f8dc585a9e5afd0f43af713ce67d8009b18efef5b6edd3'
             'b10a94df8d6c44b270cd8ea6f9af08ac803ff0a210aae602b80bbb99050f5b46'
             '78671538afa07e8efac47eadc845c1616d553e095bf749c0215fdba8af2a2c1b')
-depends=('java-runtime=11')
+depends=('java-runtime' 'java-openjfx')
+makedepends=('ant' 'git')
 optdepends=('beagle-lib')
+build(){
+    cd "$srcdir/BeastFX"
+    install -d release2/Linux/jrebin
+    ant linux -nouserlib -noinput \
+        -Drelease_dir=release2 \
+        -Dbeast2="../${pkgname}-${pkgver}" \
+        -Dbeast2path="../${pkgname}-${pkgver}" \
+        -lib "/usr/lib/jvm/default-runtime/lib/" \
+        -Dcommon_dir="../${pkgname}-${pkgver}/release/common/" \
+        -DopenjreLnx="/usr/lib/jvm/default/"
+}
 package() {
     install -dm755 "$pkgdir"/usr/{bin,share/{beast2,applications}}
-    sed -i 's/\/usr\/local\/lib/\/usr\/lib/g'  ${srcdir}/beast/bin/beast
-    mv "$srcdir"/beast/* "$pkgdir"/usr/share/beast2
+    cd "$srcdir/BeastFX/release2/Linux/"
+    cp -rf beast/* "${pkgdir}/usr/share/${pkgname}"
     for bin in $(ls $pkgdir/usr/share/beast2/bin)
 do
     ln -s /usr/share/beast2/bin/$bin ${pkgdir}/usr/bin/$bin
-done   
+done
     install -m 755 ${srcdir}/*.desktop ${pkgdir}/usr/share/applications
-}
 
+    # clear files
+    rm -rf $pkgdir/usr/share/beast2/jre
+    ln -sf /usr/lib/jvm/default/  $pkgdir/usr/share/beast2/jre
+}