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beast2: build from source

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This commit is contained in:
sukanka 2022-11-01 20:37:04 +08:00
parent 6df3b109ec
commit fb84485795
1 changed files with 28 additions and 9 deletions
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37
BioArchLinux/beast2/PKGBUILD
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@ -2,15 +2,19 @@
# Contributor: Malacology <guoyizhang at malacology dot com> # Contributor: Malacology <guoyizhang at malacology dot com>
pkgname=beast2 pkgname=beast2
pkgver=2.7.1 pkgver=2.7.2
pkgrel=1 pkgrel=1
pkgdesc="Bayesian Evolutionary Analysis by Sampling Trees. https://doi.org/10.1371/journal.pcbi.1003537" pkgdesc="Bayesian Evolutionary Analysis by Sampling Trees. https://doi.org/10.1371/journal.pcbi.1003537"
arch=('x86_64') arch=('x86_64')
url="http://www.beast2.org/" url="http://www.beast2.org/"
license=('LGPL') license=('LGPL')
provides=("beast2") source=("${pkgname}-${pkgver}.tar.gz::https://github.com/CompEvol/beast2/archive/refs/tags/${pkgver}.tar.gz"
source=("https://github.com/CompEvol/beast2/releases/download/v${pkgver}/BEAST.v${pkgver}.Linux.x86.tgz" "beauti.desktop" "densitree.desktop" "logcombiner.desktop" "treeannotator.desktop" "beast2.desktop" "loganalyser.desktop" "applauncher.desktop") "git+https://github.com/CompEvol/BeastFX.git#commit=e6c9fdb2"
sha256sums=('959ff0336a0e87637e0381aa88b22c4e9f5929319fcc69e4c5bdfadb18b97eb3' "beauti.desktop" "densitree.desktop" "logcombiner.desktop" "treeannotator.desktop" "beast2.desktop"
"loganalyser.desktop" "applauncher.desktop"
)
sha256sums=('02f561f593adf54e512d34a9366dd9e4ed0b940cb4540d97a2b4e9b705f327a3'
'SKIP'
'83fba4c776fd29d6852c9c412c31d98bff657e2d2d2763dfe46d4c6174a9495f' '83fba4c776fd29d6852c9c412c31d98bff657e2d2d2763dfe46d4c6174a9495f'
'40d86086691b6cb91d0af54e5dc53d6693e084242ff3cc77862650ca78667c3d' '40d86086691b6cb91d0af54e5dc53d6693e084242ff3cc77862650ca78667c3d'
'c2057c6ac656e13dcfbdf580a696bc79cb22c3d5270d546eac3e2fb42d620f20' 'c2057c6ac656e13dcfbdf580a696bc79cb22c3d5270d546eac3e2fb42d620f20'
@ -18,16 +22,31 @@ sha256sums=('959ff0336a0e87637e0381aa88b22c4e9f5929319fcc69e4c5bdfadb18b97eb3'
'cf09789425aec65601f8dc585a9e5afd0f43af713ce67d8009b18efef5b6edd3' 'cf09789425aec65601f8dc585a9e5afd0f43af713ce67d8009b18efef5b6edd3'
'b10a94df8d6c44b270cd8ea6f9af08ac803ff0a210aae602b80bbb99050f5b46' 'b10a94df8d6c44b270cd8ea6f9af08ac803ff0a210aae602b80bbb99050f5b46'
'78671538afa07e8efac47eadc845c1616d553e095bf749c0215fdba8af2a2c1b') '78671538afa07e8efac47eadc845c1616d553e095bf749c0215fdba8af2a2c1b')
depends=('java-runtime=11') depends=('java-runtime' 'java-openjfx')
makedepends=('ant' 'git')
optdepends=('beagle-lib') optdepends=('beagle-lib')
build(){
cd "$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() { package() {
install -dm755 "$pkgdir"/usr/{bin,share/{beast2,applications}} install -dm755 "$pkgdir"/usr/{bin,share/{beast2,applications}}
sed -i 's/\/usr\/local\/lib/\/usr\/lib/g' ${srcdir}/beast/bin/beast cd "$srcdir/BeastFX/release2/Linux/"
mv "$srcdir"/beast/* "$pkgdir"/usr/share/beast2 cp -rf beast/* "${pkgdir}/usr/share/${pkgname}"
for bin in $(ls $pkgdir/usr/share/beast2/bin) for bin in $(ls $pkgdir/usr/share/beast2/bin)
do do
ln -s /usr/share/beast2/bin/$bin ${pkgdir}/usr/bin/$bin ln -s /usr/share/beast2/bin/$bin ${pkgdir}/usr/bin/$bin
done done
install -m 755 ${srcdir}/*.desktop ${pkgdir}/usr/share/applications 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
}