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# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
DESCRIPTION="NCBI Sequence Read Archive (SRA) sratoolkit"
HOMEPAGE="https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi https://github.com/ncbi/sra-tools"
SRC_URI="https://github.com/ncbi/sra-tools/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="public-domain"
SLOT="0"
# Fix ncbi-vdb first
KEYWORDS=""
DEPEND="
sys-libs/zlib
app-arch/bzip2
dev-libs/libxml2:2=
sci-libs/hdf5
sci-biology/ngs
sci-biology/ncbi-vdb
"
RDEPEND="${DEPEND}"
S="${WORKDIR}/sra-tools-${PV}"
src_configure() {
# this is some non-standard configure script
./configure \
--with-ngs-sdk-prefix=/usr/ngs/ngs-sdk \
--with-hdf5-prefix=/usr \
|| die
}
src_install() {
dodir /usr/include
dodir /etc/profile.d
# Hard way around hard coded paths
find . -type f -exec sed -i \
-e "s:/usr/local:${ED}/usr:g" \
-e "s:/etc:${ED}/etc:g" \
-e "s:/usr/lib:${ED}/usr/lib:g" \
-e "s:/usr/include:${ED}/usr/include:g" \
-e "s:setup.py -q install:setup.py install --root="${D}":g" \
{} \; || die
default
}
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