blob: 5c35714c01d9cadededf800e19c73dd2656e81da (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
|
# Maintainer: Clint Valentine <valentine.clint@gmail.com>
pkgname=rtg-tools
pkgver=3.8.4
pkgrel=3
pkgdesc="Utilities for accurate VCF comparison and manipulation"
arch=('i686' 'x86_64')
url="https://github.com/RealTimeGenomics/rtg-tools"
license=('Simplified BSD')
depends=('java-runtime>=1.8')
makedepends=('apache-ant>1.9')
source=(
"https://github.com/RealTimeGenomics/${pkgname}/archive/${pkgver}.tar.gz"
"rtg.cfg"
"rtg.sh")
md5sums=(
'c5b558cbe845fcb315e943162b7da38e'
'1e5e1f5df474ab87b5a28a9d694e4e17'
'd7c63bf91030230c609c740d28b22d38')
build() {
cd "${srcdir}/${pkgname}-${pkgver}"
ant zip-nojre
unzip -qn dist/rtg-tools-3.8.4-*-nojre.zip
}
check() {
cd "${srcdir}/${pkgname}-${pkgver}"
ant runalltests
}
package() {
cd "${srcdir}"
# Add environment variable to specify custom location of RTG.jar
install -Dm655 rtg.cfg "${pkgdir}/etc/rtg.cfg"
echo "RTG_JAR=/usr/share/java/${pkgname}/RTG.jar" >> "${pkgdir}/etc/rtg.cfg"
# Install completion hook in profile.d to be sourced with each shell
install -Dm755 rtg.sh "${pkgdir}/etc/profile.d/rtg.sh"
# Install primary JAR file
cd "${srcdir}/${pkgname}-${pkgver}/${pkgname}-${pkgver}-"*
install -Dm655 RTG.jar "${pkgdir}/usr/share/java/${pkgname}/RTG.jar"
# Remove the need for a local configuration file, respect only system config
install -Dm755 rtg "${pkgdir}/usr/bin/rtg"
sed -i "s#\$THIS_DIR/rtg.cfg#${pkgdir}/etc/rtg.cfg#g" "${pkgdir}/usr/bin/rtg"
# Install demo script, data, and bash completions scripts
cp -r scripts "${pkgdir}/usr/share/${pkgname}"
# Licenses and documentation
install -Dm655 LICENSE.txt "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE.txt"
install -Dm655 README.txt "${pkgdir}/usr/share/doc/${pkgname}/README.txt"
install -Dm655 ReleaseNotes.txt "${pkgdir}/usr/share/doc/${pkgname}/ReleaseNotes.txt"
install -Dm655 RTGOperationsManual.pdf "${pkgdir}/usr/share/doc/${pkgname}/RTGOperationsManual.pdf"
cp -r RTGOperationsManual "${pkgdir}/usr/share/doc/${pkgname}/RTGOperationsManual"
}
|