| # Copyright 1999-2015 Gentoo Foundation |
| # Distributed under the terms of the GNU General Public License v2 |
| # $Id$ |
| |
| EAPI=5 |
| |
| MIRA_3RDPARTY_PV="06-07-2012" |
| MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat) |
| |
| inherit autotools eutils multilib |
| |
| DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina" |
| HOMEPAGE="http://www.chevreux.org/projects_mira.html" |
| SRC_URI=" |
| http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2 |
| mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" |
| # http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2 |
| # mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" |
| |
| S="${WORKDIR}"/"${PN}"-"${MY_PV}" |
| |
| SLOT="0" |
| LICENSE="GPL-2" |
| KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x86-macos" |
| IUSE="doc" |
| |
| CDEPEND=" |
| dev-libs/boost[threads] |
| dev-util/google-perftools" |
| DEPEND="${CDEPEND} |
| app-editors/vim-core |
| dev-libs/expat" |
| RDEPEND="${CDEPEND}" |
| |
| #DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED |
| # THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf ) |
| DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS ) |
| |
| src_prepare() { |
| find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die |
| epatch \ |
| "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch \ |
| "${FILESDIR}"/${P}-cout.patch |
| |
| sed \ |
| -e "s:-O[23]::g" \ |
| -e "s:-funroll-loops::g" \ |
| -i configure.ac || die |
| |
| eautoreconf |
| } |
| |
| src_configure() { |
| econf \ |
| --with-boost="${EPREFIX}/usr/$(get_libdir)" \ |
| --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \ |
| --with-boost-thread=boost_thread-mt |
| } |
| |
| #src_compile() { |
| # base_src_compile |
| # # TODO: resolve docbook incompatibility for building docs |
| # if use doc; then emake -C doc clean docs || die; fi |
| #} |
| |
| src_install() { |
| default |
| dodoc ${DOCS[@]} |
| |
| dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} |
| dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta} |
| } |
| |
| pkg_postinst() { |
| einfo "Documentation is no longer built, you can find it at:" |
| einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html" |
| } |