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# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=3
inherit eutils
W="${WORKDIR}"/"${P}"
DESCRIPTION="NCBI Sequence Read Archive (SRA) sratoolkit"
HOMEPAGE="http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=faspftp_runs_v1&m=downloads&s=download_sra"
SRC_URI="http://trace.ncbi.nlm.nih.gov/Traces/sra/static/sra_sdk-"${PV}".tar.gz"
# http://trace.ncbi.nlm.nih.gov/Traces/sra/static/sratoolkit.2.0.1-centos_linux64.tar.gz
LICENSE="public-domain"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="static"
DEPEND="app-shells/bash
sys-libs/zlib
app-arch/bzip2
dev-libs/libxml2"
RDEPEND="${DEPEND}"
# upstream says:
# icc, icpc are supported: tested with 11.0 (64-bit) and 10.1 (32-bit), 32-bit 11.0 does not work
src_compile(){
# # COMP env variable may have 'GCC' or 'ICC' values
make OUTDIR="${WORKDIR}"/objdir out || die
LIBXML_INCLUDES="/usr/include/libxml2" make dynamic || die
LIBXML_INCLUDES="/usr/include/libxml2" make release || die
LIBXML_INCLUDES="/usr/include/libxml2" emake || die
}
src_install(){
rm -rf /var/tmp/portage/sci-biology/"${P}"/image//var
# BUG: at the moment every binary is installed three times, e.g.:
# -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump
# -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump.2
# -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump.2.1.6
if use amd64; then
builddir="x86_64"
elif use x86; then
builddir="i386"
fi
mkdir "${D}"/usr
mkdir "${D}"/usr/bin
mkdir -p "${D}"/usr/lib/ncbi
mkdir -p "${D}"/usr/ncbi/schema
for f in "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/bin/*; do cp --preserve=links "$f" "${D}"/usr/bin || die "copy failed" ; done
dolib "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/*
# install the main libs and the ncbi/vdb-copy.kfg file
insinto /usr/lib/ncbi
doins "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/ncbi/*
insinto /usr/ncbi/schema
doins "${W}"/interfaces/align/*.vschema
doins "${W}"/interfaces/sra/*.vschema
doins "${W}"/interfaces/vdb/*.vschema
doins "${W}"/interfaces/ncbi/*.vschema
doins "${W}"/interfaces/insdc/*.vschema
}
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