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# Maintainer: ZJLIN <zjin841126@gmail.com> | ||
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net> | ||
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pkgname=trimmomatic | ||
_pkgname=Trimmomatic | ||
pkgver=0.39 | ||
pkgrel=5 | ||
pkgrel=6 | ||
pkgdesc='Trimmomatic: A flexible read trimming tool for Illumina NGS data' | ||
arch=('any') | ||
url="http://www.usadellab.org/cms/?page=trimmomatic" | ||
license=('GPL3') | ||
depends=('java-runtime>=6') | ||
source=("http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-$pkgver.zip" | ||
"trimmomatic" | ||
depends=('java-runtime') | ||
makedepends=('java-environment=11' 'ant') | ||
source=("https://github.com/usadellab/Trimmomatic/archive/refs/tags/v${pkgver}.tar.gz" | ||
"$pkgname" | ||
"$pkgname.patch" | ||
) | ||
md5sums=('271ed9dca91132eee0c960e0ae487bcd' | ||
'acd57c8656a1a398b42b50677a79df9c') | ||
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md5sums=('2f80c01dd0876f7761b33ed77768a76c' | ||
'0716cd4695be3e8ea6d4a5aa78f7eb85' | ||
'4612f0187c29f7be68433778f884a067') | ||
prepare() { | ||
cd $_pkgname-$pkgver | ||
patch -N -i $srcdir/$pkgname.patch | ||
} | ||
build() { | ||
cd $_pkgname-$pkgver | ||
ant | ||
} | ||
package() { | ||
mkdir -p $pkgdir/usr/share/java/${pkgname} | ||
cp -rf $srcdir/Trimmomatic-$pkgver/* $pkgdir/usr/share/java/${pkgname} | ||
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install -Dm755 $srcdir/trimmomatic -t $pkgdir/usr/bin | ||
install -Dm 755 $srcdir/$_pkgname-$pkgver/dist/jar/$pkgname-$pkgver.jar $pkgdir/usr/share/java/$pkgname/$pkgname.jar | ||
install -Dm 755 $srcdir/$pkgname -t $pkgdir/usr/bin | ||
} |
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#!/usr/bin/bash | ||
exec /usr/bin/java -jar /usr/share/java/trimmomatic/trimmomatic-0.39.jar "$@" | ||
exec /usr/bin/java -jar /usr/share/java/trimmomatic/trimmomatic.jar "$@" |
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diff --git a/build.xml b/build.xml | ||
index 2efbac2..5d57a05 100644 | ||
--- a/build.xml | ||
+++ b/build.xml | ||
@@ -31,7 +31,7 @@ | ||
</target> | ||
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<target name="compile" depends="import"> | ||
- <javac srcdir="${src}" destdir="${dist_build}" debug="true" source="1.5" target="1.5" includeantruntime="false"> | ||
+ <javac srcdir="${src}" destdir="${dist_build}" debug="true" source="11" target="11" includeantruntime="false"> | ||
<classpath> | ||
<fileset dir="${dist_lib}"> | ||
<include name="*.jar" /> |