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pkgname=gatk
pkgver=4.6.0.0
pkgrel=1
pkgdesc="Genome Analysis Toolkit https://doi.org/10.1101/gr.107524.110"
arch=('any')
url=https://software.broadinstitute.org/"${pkgname}"
license=('BSD')
makedepends=('git' 'java-environment=17' 'git-lfs')
depends=('java-runtime=17' 'python' 'r')
source=("gatk.sh")
sha256sums=('acc059e37c9e9e9053815095d3eecd00cd115d22f4c14bc4b97d7a5be13234c4')
prepare() {
cd "${srcdir}"
git clone https://github.com/broadinstitute/gatk.git "${pkgname}"
cd $pkgname
git checkout "${pkgver}"
git lfs install
}
build() {
cd "${srcdir}"/"${pkgname}"
./gradlew localJar
}
package() {
install -Dm755 gatk.sh "${pkgdir}"/usr/bin/gatk
cd "${srcdir}"/"${pkgname}"
install -Dm644 build/libs/gatk-package-"${pkgver}"-SNAPSHOT-local.jar "${pkgdir}"/usr/share/java/"${pkgname}"/GenomeAnalysisTK.jar
}
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