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# Copyright 1999-2017 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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EAPI=6
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MIRA_3RDPARTY_PV="06-07-2012"
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MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat)
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inherit autotools eutils multilib
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DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Illumina"
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HOMEPAGE="http://www.chevreux.org/projects_mira.html"
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SRC_URI="
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https://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2
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mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
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# https://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2
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# mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
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S="${WORKDIR}"/"${PN}"-"${MY_PV}"
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SLOT="0"
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LICENSE="GPL-2"
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KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x86-macos"
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IUSE="doc"
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CDEPEND="
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dev-libs/boost[threads]
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dev-util/google-perftools"
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DEPEND="${CDEPEND}
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sys-devel/flex
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app-editors/vim-core
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dev-libs/expat"
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RDEPEND="${CDEPEND}"
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#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED
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# THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf )
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DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS )
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PATCHES=(
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"${FILESDIR}/${PN}-4.0.2-boost-1.50.patch"
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"${FILESDIR}/${PN}-4.0.2-cout.patch"
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"${FILESDIR}/${PN}-4.0.2-cmath.patch"
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)
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src_prepare() {
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find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
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default
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sed \
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-e "s:-O[23]::g" \
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-e "s:-funroll-loops::g" \
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-i configure.ac || die
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eautoreconf
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# Remove C++ source files that upstream built with flex.
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local f
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local PREBUILT_CXX_LEXER_FILES=(
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"${S}"/src/caf/caf_flexer.cc
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"${S}"/src/io/exp_flexer.cc
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"${S}"/src/mira/parameters_flexer.cc
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)
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for f in "${PREBUILT_CXX_LEXER_FILES[@]}"; do
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if [[ -f ${f} ]] ; then
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rm "${f}" || die "Failed to remove ${f}"
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else
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die "${f} not found"
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fi
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done
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}
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src_configure() {
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econf \
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--with-boost="${EPREFIX}/usr/$(get_libdir)" \
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--with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \
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--with-boost-thread=boost_thread-mt
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}
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#src_compile() {
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# base_src_compile
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# # TODO: resolve docbook incompatibility for building docs
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# use doc && emake -C doc clean docs
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#}
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src_install() {
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default
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dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
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dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta}
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}
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pkg_postinst() {
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einfo "Documentation is no longer built, you can find it at:"
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einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html"
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}
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