From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 452F41381F3 for ; Wed, 25 Sep 2013 13:35:41 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 9A621E0B89; Wed, 25 Sep 2013 13:35:36 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 14DE9E0B89 for ; Wed, 25 Sep 2013 13:35:35 +0000 (UTC) Received: from hornbill.gentoo.org (hornbill.gentoo.org [94.100.119.163]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id EF38733E9DB for ; Wed, 25 Sep 2013 13:35:34 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id E913DE5309 for ; Wed, 25 Sep 2013 13:35:31 +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: <1380116209.bc1bf424a20c10b9a2ae6e2bfd337d47173e3810.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/mira/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/mira/mira-4.0_rc2.ebuild X-VCS-Directories: sci-biology/mira/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: bc1bf424a20c10b9a2ae6e2bfd337d47173e3810 X-VCS-Branch: master Date: Wed, 25 Sep 2013 13:35:31 +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: 846c43c4-7e75-4aff-abde-d7621dfc8b63 X-Archives-Hash: c05f16bf5331cfb4a2afd7f89aad7512 commit: bc1bf424a20c10b9a2ae6e2bfd337d47173e3810 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Wed Sep 25 13:36:49 2013 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed Sep 25 13:36:49 2013 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bc1bf424 version bump --- sci-biology/mira/mira-4.0_rc2.ebuild | 76 ++++++++++++++++++++++++++++++++++++ 1 file changed, 76 insertions(+) diff --git a/sci-biology/mira/mira-4.0_rc2.ebuild b/sci-biology/mira/mira-4.0_rc2.ebuild new file mode 100644 index 0000000..13df7b7 --- /dev/null +++ b/sci-biology/mira/mira-4.0_rc2.ebuild @@ -0,0 +1,76 @@ +# 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-3.9.18.ebuild,v 1.1 2013/07/07 19:41:05 jlec Exp $ + +EAPI=5 + +MIRA_3RDPARTY_PV="06-07-2012" + +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/mira-4.0rc2.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}/mira-4.0rc2" + +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 + + ln -s config/m4 . + AT_M4DIR="config/m4" eaclocal + 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() { + 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" +}