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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
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-"${PV}".tar.gz"
# http://trace.ncbi.nlm.nih.gov/Traces/sra/static/sratoolkit.2.0.1-centos_linux64.tar.gz
LICENSE="public-domain"
SLOT="0"
#KEYWORDS=""
KEYWORDS="~amd64 ~x86"
IUSE="static"
DEPEND="app-shells/bash
sys-libs/zlib
app-arch/bzip2
dev-libs/libxml2"
RDEPEND="${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_prepare(){
epatch "${FILESDIR}"/sra_sdk-destdir.patch || die
}
src_compile(){
# -I/usr/include/libxml2
# -I/var/tmp/portage/sci-biology/sra_sdk-2.0.1/work/sra_sdk-2.0.1/interfaces/os/unix
# COMP env variable may have 'GCC' or 'ICC' values
if use static; then
emake static LIBDIR=/lib64 DESTDIR="${D}"
else
emake dynamic LIBDIR=/lib64 DESTDIR="${D}"
fi
LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir out LIBDIR=/lib64 DESTDIR="${D}" || die
LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir LIBDIR=/lib64 DESTDIR="${D}" || die
}
src_install(){
# for details see "${WORKDIR}"/sra_sdk-2.1.6/README-build
# 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
dobin "${WORKDIR}"/objdir/linux/pub/gcc/x86_64/bin/*
insinto /usr/bin/ncbi
dobin "${WORKDIR}"/objdir/linux/pub/gcc/x86_64/bin/ncbi/*
elif use x86; then
dobin "${WORKDIR}"/objdir/linux/pub/gcc/i386/bin/*
insinto /usr/bin/ncbi
dobin "${WORKDIR}"/objdir/linux/pub/gcc/i386/bin/ncbi/*
fi
# mkdir -p ${D}/usr/bin || die
# for f in ${W}/objdir/linux/rel/gcc/i386/bin/*; do if [ ! -l "$f" ]; then cp "$f" ${D}/usr/bin || die "copy failed" ; fi; done
# looks the binaries have the folllowing libs statically linked in so we do NOT need these files
# mkdir -p ${D}/usr/ilib || die
# dolib ${W}/objdir/linux/rel/gcc/i386/ilib/*
# insinto "${D}"/usr/lib/ncbi
# doins ${W}/objdir/linux/rel/gcc/i386/ilib/ncbi/*
# mkdir -p ${D}/usr/lib || die
# dolib ${W}/objdir/linux/rel/gcc/i386/lib/*
# insinto "${D}"/usr/lib/ncbi
# doins ${W}/objdir/linux/rel/gcc/i386/lib/ncbi/*
# same for mod/ and wmod/ subdirs
}
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