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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="Fix assembled reference using BAM-aligned reads, call SNPs"
HOMEPAGE="
https://github.com/broadinstitute/pilon
https://github.com/broadinstitute/pilon/wiki"
SRC_URI="https://github.com/broadinstitute/pilon/releases/download/v${PV}/pilon-${PV}.jar"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64"
# contains bundled sbt-assembly module
DEPEND=">=virtual/jdk-1.7:*"
RDEPEND="${DEPEND}
>=virtual/jre-1.7:*
>=dev-java/htsjdk-1.130"
S="${WORKDIR}"
src_install(){
cp -p "${DISTDIR}"/pilon-${PV}.jar . || die
java-pkg_dojar pilon-${PV}.jar
}
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