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# Maintainer: Guoyi Zhang <guoyi zhang at malacology dot net>
# Contributor: Grey Christoforo <first name at last name dot net>
pkgname=picard-tools
_pkgname=picard
pkgver=3.3.0
pkgrel=1
pkgdesc='set of tools for working with next generation sequencing data in the BAM format'
arch=(any)
url="https://github.com/broadinstitute/picard"
license=(MIT)
depends=('java-runtime=17')
makedepends=('ant' 'git' 'java-environment=17')
source=("git+${url}.git#tag=${pkgver}")
sha256sums=('f43e3cf9c4d367774e03220b169599c178721ef031f0e2014beda33e41127645')
build(){
cd $_pkgname
./gradlew shadowJar
}
package() {
echo "java -jar /usr/share/$_pkgname/picard.jar \$@" >> $_pkgname-java
chmod +x $_pkgname-java
install -Dm 755 $_pkgname-java $pkgdir/usr/bin/$_pkgname-java
install -Dm 755 $srcdir/$_pkgname/build/libs/picard.jar $pkgdir/usr/share/$_pkgname/picard.jar
}
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