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# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
inherit java-pkg-2
DESCRIPTION="Illumina adapter trimming tool"
HOMEPAGE="http://www.usadellab.org/cms/?page=trimmomatic"
SRC_URI="
http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-Src-${PV}.zip
http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf -> "${P}"_manual.pdf"
# http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64"
DEPEND=">=virtual/jdk-1.7:*
app-arch/unzip"
RDEPEND=">=virtual/jre-1.7:*"
src_prepare() {
sed -i -E 's/source="[0-9\.]+"//g' build.xml || die
sed -i -E 's/target="[0-9\.]+"//g' build.xml || die
default
}
src_compile() {
eant dist \
-Dant.build.javac.source="$(java-pkg_get-source)" \
-Dant.build.javac.target="$(java-pkg_get-target)"
}
src_install() {
java-pkg_newjar "dist/jar/${P}.jar" "${PN}.jar"
insinto /usr/share/${PN}/Illumina
doins adapters/*.fa
dodoc "${DISTDIR}"/${P}_manual.pdf
}
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