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# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
inherit java-pkg-2 java-ant-2
DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize, FASTA/Q tool"
HOMEPAGE="http://sourceforge.net/projects/bbmap/"
SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"
LICENSE="BSD"
SLOT="0"
KEYWORDS="~amd64"
IUSE=""
DEPEND="
sys-cluster/openmpi[java]
>=virtual/jdk-1.7:*
dev-java/ant-core"
RDEPEND="${DEPEND}
>=virtual/jre-1.7:*"
S="${WORKDIR}"/bbmap
src_prepare(){
# fix the line in build.xml to point to mpi.jar location
# <property name="mpijar" location="/tmp/mpi.jar" ></property>
# see bug #542700
sed -e 's#/usr/common/usg/hpc/openmpi/gnu4.6/sge/1.8.1/ib_2.1-1.0.0/lib/mpi.jar#/usr/share/openmpi/lib/mpi.jar#' -i build.xml
sed -e 's#compiler="${jcompiler}" ##' -i build.xml
epatch "${FILESDIR}"/UnicodeToAscii.patch
}
src_compile(){
ant dist || die
}
src_install(){
dobin *.sh
dodoc docs/readme.txt
java-pkg_dojar dist/lib/BBTools.jar
}
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