# Maintainer: Clint Valentine pkgname=fgbio-git pkgver=0.4.0.r21.gc45e26f pkgrel=1 pkgdesc="Tools for working with genomic and high throughput sequencing data." arch=('any') url="https://github.com/fulcrumgenomics/fgbio" license=('MIT') depends=('git-lfs' 'java-runtime>=8' 'sbt' 'scala>=2.12') checkdepends=('r' 'r-cran-ggplot2') provides=('fgbio') conflicts=('fgbio') source=("fgbio.sh") md5sums=("6be7f08531588d04c3417da9e35c9e84") prepare() { # Git LFS fails when used as a 'source' if [[ -d fgbio ]]; then cd fgbio && git pull; else git clone https://github.com/fulcrumgenomics/fgbio.git; fi } pkgver() { cd "fgbio" git describe --long --tags | sed 's/\([^-]*-g\)/r\1/;s/-/./g' } build() { cd "${srcdir}/fgbio" sbt assembly } check() { cd "${srcdir}/fgbio" sbt test } package() { cd "${srcdir}/fgbio" install -Dm644 target/scala-2.12/fgbio*.jar "${pkgdir}/usr/share/java/fgbio/fgbio.jar" install -Dm644 LICENSE "${pkgdir}/usr/share/licenses/fgbio/LICENSE" install -Dm644 README.md "${pkgdir}/usr/share/doc/fgbio/README.md" cd "${srcdir}" install -Dm755 "fgbio.sh" "${pkgdir}/usr/bin/fgbio" }