commit: 97b1cf9bacba1cede303203987f487a1290bc60e Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sat Apr 12 12:28:06 2014 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sat Apr 12 12:28:06 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=97b1cf9b
sci-biology/mira-4.0.1: bump to current recommended bugfix release Package-Manager: portage-2.2.7 --- sci-biology/mira/ChangeLog | 5 +++ sci-biology/mira/mira-4.0.1.ebuild | 76 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 81 insertions(+) diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog index 4dd3e5b..b5f200e 100644 --- a/sci-biology/mira/ChangeLog +++ b/sci-biology/mira/ChangeLog @@ -2,6 +2,11 @@ # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*mira-4.0.1 (12 Apr 2014) + + 12 Apr 2014; Martin Mokrejs <[email protected]> +mira-4.0.1.ebuild: + sci-biology/mira-4.0.1: bump to current recommended bugfix release + 06 Jan 2014; Justin Lecher <[email protected]> -mira-3.4.0.1.ebuild, -mira-3.4.1.1.ebuild, -mira-3.9.9.ebuild, -mira-3.9.15.ebuild, -mira-4.0_rc2.ebuild, mira-4.0_rc4.ebuild: diff --git a/sci-biology/mira/mira-4.0.1.ebuild b/sci-biology/mira/mira-4.0.1.ebuild new file mode 100644 index 0000000..f9c38fa --- /dev/null +++ b/sci-biology/mira/mira-4.0.1.ebuild @@ -0,0 +1,76 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +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}"-"${MY_PV}" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" +IUSE="doc" + +CDEPEND=" + dev-libs/boost + dev-util/google-perftools" +DEPEND="${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}"/${PN}-3.4.0.2-boost-1.50.patch + + sed \ + -e "s:-O[23]::g" \ + -e "s:-funroll-loops::g" \ + -i configure.ac || die + + eautoreconf +} + +src_configure() { + econf \ + --with-boost="${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"; +}
