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# Maintainer: Clint Valentine <valentine.clint@gmail.com>
pkgname=bbmap
pkgver=39.13
pkgrel=1
pkgdesc="A short read aligner and other bioinformatic tools"
arch=('x86_64')
url=https://jgi.doe.gov/data-and-tools/bbtools/
license=('BSD')
depends=('java-environment')
optdepends=(
'env-modules: for any scripts requiring `module`'
'pigz: for parallel GZIP (de)compression'
'samtools: for BAM output'
)
source=("${pkgname}"-"${pkgver}".tar.gz::https://downloads.sourceforge.net/project/"${pkgname}"/BBMap_"${pkgver}".tar.gz)
sha256sums=('6920a94549d3fca129e031cc14e5306ae571a223410e1f116b0292e530c433de')
build() {
cd "${srcdir}"/"${pkgname}"/jni
make -f makefile.linux clean
}
package() {
cd "${srcdir}"/"${pkgname}"/jni
archlinux-java fix
# Headers for JNI are found in this Arch Linux specific location
env JAVA_HOME=/usr/lib/jvm/default make -f makefile.linux
cd "${srcdir}"/"${pkgname}"
mkdir -p "${pkgdir}"/usr/share/doc/"${pkgname}"/
cp -r docs/* "${pkgdir}"/usr/share/doc/"${pkgname}"/
mkdir -p "${pkgdir}"/usr/share/java/"${pkgname}"/
cp -r config "${pkgdir}"/usr/share/java/"${pkgname}"/
cp -r current "${pkgdir}"/usr/share/java/"${pkgname}"/
cp -r jni "${pkgdir}"/usr/share/java/"${pkgname}"/
cp -r pipelines "${pkgdir}"/usr/share/java/"${pkgname}"/
cp -r resources "${pkgdir}"/usr/share/java/"${pkgname}"/
for script in *.sh; do
sed -i s_'\bCP=.*'_CP=/usr/share/java/"${pkgname}"/current/_ "${script}"
sed -i s_'\bDIR=.*'_DIR=/usr/bin/_ "${script}"
sed -i s_'\bNATIVELIBDIR=.*'_NATIVELIBDIR=/usr/share/java/"${pkgname}"/current/jni/_ "${script}"
install -Dm775 "${script}" "${pkgdir}"/usr/bin/"${script}"
done
}
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