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Tue, 30 Apr 2013 09:42:51 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1367314938.00bb77fe4833272c18c448942d8e19b99d729e77.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/mira/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/mira/ChangeLog sci-biology/mira/mira-3.9.15.ebuild X-VCS-Directories: sci-biology/mira/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 00bb77fe4833272c18c448942d8e19b99d729e77 X-VCS-Branch: master Date: Tue, 30 Apr 2013 09:42:51 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 73e7d7dd-ebff-4711-ac82-a132dc10a905 X-Archives-Hash: 20c2789e5bb99fe68d0289f42c149c10 commit: 00bb77fe4833272c18c448942d8e19b99d729e77 Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Tue Apr 30 09:42:18 2013 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Tue Apr 30 09:42:18 2013 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=00bb77fe sci-biology/mira-3.9.15: bump to current besta version Package-Manager: portage-2.1.11.62 --- sci-biology/mira/ChangeLog | 6 +++ sci-biology/mira/mira-3.9.15.ebuild | 64 +++++++++++++++++++++++++++++++++++ 2 files changed, 70 insertions(+), 0 deletions(-) diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog index 68b66f6..afda6bd 100644 --- a/sci-biology/mira/ChangeLog +++ b/sci-biology/mira/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*mira-3.9.15 (30 Apr 2013) + + 30 Apr 2013; Martin Mokrejs + +mira-3.9.15.ebuild: + sci-biology/mira-3.9.15: bump to current besta version mira-3.9.15.ebuild + *mira-3.4.1.1 (22 Feb 2013) *mira-3.9.9 (22 Feb 2013) diff --git a/sci-biology/mira/mira-3.9.15.ebuild b/sci-biology/mira/mira-3.9.15.ebuild new file mode 100644 index 0000000..8dbb921 --- /dev/null +++ b/sci-biology/mira/mira-3.9.15.ebuild @@ -0,0 +1,64 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.4.0.2.ebuild,v 1.1 2012/11/07 22:29:56 jlec Exp $ + +EAPI=4 + +MIRA_3RDPARTY_PV="06-07-2012" + +inherit autotools base 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/development/${P}.tar.bz2 + mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" + +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 + AT_M4DIR="config/m4" 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() { + base_src_install + 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" +}